does the same outcome occur or is this only problematic when the collection is empty.

As a quick follow-up, this does only seem to be problematic in this corner case where the persist and merge of the entity occur when the element-collection is empty. If the element-collection is not-empty, then we continue to mark the collection's MOD field as being modified. I have a hunch this may likely be an issue where we treat null synonymous with an empty-collection which leads to this tricky corner case but I need to step through the debugger to be sure. Either way, it should be relatively simple to resolve.