Logging in is not the condition to reset timer.
You have to look at your base timer with a repair hammer and make sure the server registers that you are touching it. Sometimes it can take up to a minute to reset.
To force a faster reset, place or remove a placeble.
Perhaps he logged in a bit past the decay timer and lost his thralls because they depend on a fix absolute timer that doesn’t seem to fluctuate with server lag or resets.
Theory : 1) His base might have already been in decay state when he logged in the first time without the timer reset registering properly. Then the next time he logged in past the thrall timer and they all decayed.
2) He lost the base first because of the same reason but then players came in and killed his thralls using mobs or other methods.