lower prison reset

I had made it all the way to brutus in warden quarters and when I died I came back to the waypoint for the lower prison and it completely reset, had to find the way to upper prison and clear out monsters again. When I found the upper prison it was not reset...

That sounds entirely possible given that it could take more than 15 minutes after you left the lower prison but within 15 minutes of leaving Brutus (that's still upper prison)