It's happened again. I think I can narrow it down a tiny bit. So this didn't happen for me during last few updates that didn't have the "optimizing your apps ..." -> "tap to restart all apps" thingy, this didn't show up. I updated to A16 and got the "optimizing your apps ..." thingy after the reboot. Until that ran the SMS app was fine. However once that concludes and you hit that tap-to-restart-apps notification, go back to the secondary profile where the sms/calls are allowed, you see the problem mention in this thread.
Go back to owner profile -> toggle off sms/phone allowance for those 2ndary profiles that were allowed this and also toggle off "allow session to run in background" (which I think just kills that session?) -> go one step back (I'm imagining this is needed for the changes to take effect, not sure -> come back to the toggle page -> toggle on the sms/phone calls and allow session to run in the background -> finally go to the affected profile, will have to login with pin/password as it was killed -> sms/calls work fine.
I'll wait for the next update to test this again, but I'm fairly certain now that this happens when I tap-to-restart the optimized apps.