Why isn't Device.hints persistent between upgrades?
This isn't just 2.1, but even back on 2.0.1 and earlier, its always been a PITA to make sure the system doesn't reboot after an upgrade so I can get a chance to disable ACPI on my particular hardware so that the system successfully restarts after the upgrade. Why is this file overwritten? Surely an upgrade should leave the existing file in place for situations such as mine?
ACPI can be disabled through /boot/loader.conf.local which should survive upgrades. See the FreeBSD man page on loader.conf for a description of the significance of /boot/loader.conf.local.
See description of loader variable hint.acpi.0.disabled in the FreeBSD man page on ACPI at (for example) http://www.freebsd.org/cgi/man.cgi?query=acpi&apropos=0&sektion=0&manpath=FreeBSD+9.0-RELEASE+and+Ports&arch=default&format=html