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
b9edd2e02e