I just upgraded one system (non HA) without removing the packages and it came up just fine and reinstalled the packages. I did see some errors in the logs related to snort and pbi but right after that it mentioned uninstalling and then re-installing snort and it came up just fine on it's own just like a good little firewall.
Seems to have worked perfectly. I am doing the same thing on a cluster now locally. Upgrading the secondary first and will test for awhile on the secondary before going back to the primary.
Jun 17 17:07:59 check_reload_status: Starting packages
Jun 17 17:08:04 php: : Restarting/Starting all packages.
Jun 17 17:08:12 php: : rc.newwanip: Informational is starting ovpns1.
Jun 17 17:08:12 php: : rc.newwanip: on (IP address: 192.168.x.1) (interface: ) (real interface: ovpns1).
Jun 17 17:08:12 check_reload_status: Reloading filter
Jun 17 17:08:13 php: : pfSense package system has detected an ip change -> 192.168.x.1 ... Restarting packages.
Jun 17 17:08:13 check_reload_status: Starting packages
Jun 17 17:08:16 php: : Restarting/Starting all packages.
Jun 17 17:08:18 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:18 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:18 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:18 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:18 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:20 php: : Could not find the libsf_ftptelnet_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_smtp_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:20 php: : Could not find the libsf_pop_preproc file. Snort might error out!
Jun 17 17:08:21 php: : Could not find the libsf_imap_preproc file. Snort might error out!
Jun 17 17:08:21 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:29 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:29 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:29 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:29 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:29 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:31 php: : Restarting/Starting all packages.
Jun 17 17:08:31 php: : Could not find the libsf_ftptelnet_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_smtp_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_pop_preproc file. Snort might error out!
Jun 17 17:08:31 php: : Could not find the libsf_imap_preproc file. Snort might error out!
Jun 17 17:08:31 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:32 check_reload_status: Syncing firewall
Jun 17 17:08:35 php: : PBI dir for zip-3.0-i386 was not found - cannot cleanup PBI files
Jun 17 17:08:35 php: : PBI dir for p7zip-9.20.1-i386 was not found - cannot cleanup PBI files
Jun 17 17:08:41 SnortStartup[52268]: Snort START for Lan(22290_rl1)...
Jun 17 17:08:41 php: : Beginning package installation for OpenVPN Client Export Utility .
Jun 17 17:08:41 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:41 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:41 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:41 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:41 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:42 check_reload_status: Syncing firewall
Jun 17 17:08:43 php: : Could not find the libsf_ftptelnet_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_smtp_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_ssl_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_sip_preproc file. Snort might error out!
Jun 17 17:08:43 snort[52668]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules": No such file or directory.
Jun 17 17:08:43 php: : Could not find the libsf_dce2_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_dns_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_pop_preproc file. Snort might error out!
Jun 17 17:08:43 php: : Could not find the libsf_imap_preproc file. Snort might error out!
Jun 17 17:08:43 php: : [Snort] Seems preprocessor/decoder rules are missing, enabling autogeneration of them
Jun 17 17:08:45 SnortStartup[76208]: Snort START for Lan(22290_rl1)...
Jun 17 17:08:46 SnortStartup[85053]: Snort START for Wan(7417_rl0)...
Jun 17 17:08:47 snort[96411]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules": No such file or directory.
Jun 17 17:08:47 snort[82686]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules": No such file or directory.
Jun 17 17:08:49 SnortStartup[10729]: Snort START for Wan(7417_rl0)...
Jun 17 17:08:49 snort[11057]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules": No such file or directory.
Jun 17 17:08:55 SnortStartup[36283]: Snort START for Lan(22290_rl1)...
Jun 17 17:08:55 snort[36584]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_22290_rl1//usr/pbi/snort-i386/etc/snort/snort_22290_rl1/rules/snort.rules": No such file or directory.
Jun 17 17:08:58 SnortStartup[43686]: Snort START for Wan(7417_rl0)...
Jun 17 17:08:58 check_reload_status: Syncing firewall
Jun 17 17:09:02 snort[45025]: FATAL ERROR: /usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules(0) Unable to open rules file "/usr/pbi/snort-i386/etc/snort/snort_7417_rl0//usr/pbi/snort-i386/etc/snort/snort_7417_rl0/rules/snort.rules": No such file or directory.
Jun 17 17:09:36 php: : PBI dir for snort-2.9.4.1-i386 was not found - cannot cleanup PBI files
Jun 17 17:09:37 check_reload_status: Syncing firewall
Jun 17 17:09:38 php: : [Snort] Snort package uninstall in progress...
Jun 17 17:09:46 php: : [Snort] Package deletion requested... removing all files...
Jun 17 17:09:48 check_reload_status: Syncing firewall
Jun 17 17:09:49 php: : Beginning package installation for snort .
Jun 17 17:10:25 php: /index.php: Successful login for user 'admin' from: 192.168.y.3
Jun 17 17:10:25 php: /index.php: Successful login for user 'admin' from: 192.168.y.3
Jun 17 17:10:42 php: : [Snort] Saved settings detected... rebuilding installation with saved settings...
Jun 17 17:10:42 php: : [Snort] Downloading and updating configured rule types...
Jun 17 17:10:44 php: : [Snort] There is a new set of Snort VRT rules posted. Downloading...
Jun 17 17:11:08 php: /index.php: Successful login for user 'admin' from: 97.z.z.z
Jun 17 17:11:08 php: /index.php: Successful login for user 'admin' from: 97.z.z.z
Jun 17 17:12:03 php: : [Snort] There is a new set of Snort GPLv2 Community Rules posted. Downloading...
Jun 17 17:12:04 php: : [Snort] Snort GPLv2 Community Rules file update downloaded successfully
Jun 17 17:12:05 php: : [Snort] There is a new set of EmergingThreats rules posted. Downloading...
Jun 17 17:12:06 php: : [Snort] EmergingThreats rules file update downloaded successfully
Jun 17 17:12:29 php: : [Snort] The Rules update has finished.
Jun 17 17:12:29 php: : [Snort] Updating rules configuration for: LAN ...
Jun 17 17:13:00 php: : [Snort] Enabling any flowbit-required rules for: LAN...
Jun 17 17:13:03 php: : [Snort] Building new sig-msg.map file for LAN...
Jun 17 17:13:11 php: : [Snort] Updating rules configuration for: WAN ...
Jun 17 17:13:11 php: : [Snort] Warning - no text rules selected for: WAN ...
Jun 17 17:13:11 php: : [Snort] Building new sig-msg.map file for WAN...
Jun 17 17:13:11 php: : [Snort] Finished rebuilding installation from saved settings...
Jun 17 17:13:11 php: : [Snort] Package post-installation tasks completed...
Jun 17 17:13:13 check_reload_status: Syncing firewall
Jun 17 17:13:14 syslogd: exiting on signal 15
Jun 17 17:13:15 syslogd: kernel boot file is /boot/kernel/kernel
Jun 17 17:13:16 php: : Restarting/Starting all packages.
Jun 17 17:13:28 SnortStartup[90969]: Snort START for Lan(22290_rl1)...
Jun 17 17:13:29 login: login on ttyv1 as root
Jun 17 17:13:29 sshlockout[95402]: sshlockout/webConfigurator v3.0 starting up
Jun 17 17:13:29 login: login on ttyv0 as root
Jun 17 17:16:51 kernel: rl1: promiscuous mode enabled
Jun 17 17:16:54 SnortStartup[40873]: Snort START for Wan(7417_rl0)...