Curiously, I may have encountered something similar after the recent update. Do the non-boss crocs not spawn or do they fail to respawn?
Possibly, the latter is a thing now. I also have a base near a boss (demon spider on Siptah), but in enough of distance so that it didn’t affect the area before Age of War.
I killed the spiders and the boss while extending my base, and noticed that the boss respawned several times, but not the regular spiders, or they failed to respawn at all.
That was on single player, though, and may have been some weird effect of the limited rendering distance. Sounds similar to this report, though, so maybe there’s something to it.