It looks like the "user edited flag propagation" node built for the geometry nodes modifier is unchanged after modifiers are removed. My guess is this is now a more general problem when modifiers are removed-- I guess the depsgraph nodes for an object have to be rebuilt when that happens now. Maybe there is a more general fix, but to fix the crash mentioned in the report, I tagged the depsgraph for a relations update, which rebuilds the problematic modifier node. Pull Request: https://projects.blender.org/blender/blender/pulls/124252