This issue has not reappeared in the last few days, and it used to occur at least once a day.
The only major change to my configurations is to improve the stability of the PPPoE link to the Internet. I was using a USB Ethernet adapter for my PPPoE link and the link was quite unstable, typical PPPoE uptimes were a few hours max. I have since changed to a VLAN based solution to get my PPPoE traffic out of the pfsense environment. The result of this is that the PPPoE is now significantly more stable and at the same time the IPsec phase1 without phase 2 problem appears to have gone away.
As well as being more stable the time to reconnect when the PPPoE link does fail has increased. With the USB Ethernet adapter the PPPoE Daemon would receive a TERM signal, shutdown, and then immediately reconnect. Now all the PPPoE outages look more like ISP issues and are loss of LCP echo, followed by a few attempts to reconnect. So the PPPoE link is down for a much longer time and does not instantly reconnect.
So at this stage it looks like the IPsec loss of phase 2 may relate to the manner/frequency of link failure on the Internet link.
I have left the IPsec links in IKEv1 and if the issue occurs again then I will hopefully be able to supply the appropriate logging information.
Tim