Saving .ai file, then 'Save as' to .pdf too quickly and Illustrator abandons saving the .ai file

I have been working on some packaging in Illustrator and have noticed that when I makes changes to the .ai document and then go to save out a .pdf file BEFORE the .ai file has finished saving, Illustrator will abandon saving the .ai file and save the .pdf file instead.

This has subsequently caused issues where the original .ai file is not updated, although the .pdf proof is fine.

I am now having to wait until the .ai file has finished saving before attempting to save the file as a .pdf.

This did not happen in previous versions.

Has anyone else come across this issue?