thanks, I have something similar, will try to reproduce
edit: @Tom_P looks like I know how to reproduce:
Open a file
make an edit and undo (Document still stays Edited)
SaveSmall
result:
Document Edit state doesn’t change
After a few seconds this will make the popup appear as you mentioned.
Does this match with what you’re seeing?
logged as RH-71606 SaveSmall doesn’t update document edited status