The commit in the comment above is definitely the cause. Pinning down the exact problem is slightly trickier.
I have tried several obvious looking changes from the diff with no success.
The major change however, appears to be that the MappingImpl no longer gets a classLoader per class as was introduced in the change from LDEV-4739 which fixed this very same issue from the conversation at Classloading: steadily increases (Lucee 5.4.3.x)
Instead, we get a class loader per physical directory once again and the issue returns. Obviously, there are lots more things going on and I’m trying to pick it apart but its pretty tricky.