Somewhat continuing the conversation from here but starting a new one given the time elapsed Bug Report: Saving Issues
I am experiencing the same problem. When I tried deleting the original file and re-did the export, I got an error saying I did not have access to save that file. When I then retried (still no sign of the file in Explorer) it told me that I was replacing the file and still not saving although it tells me it has.
Adobe Air Version: WIN 32,0,0,100
It seems to happen randomly - some exports from the same project save with no problems, overwriting the existing version.
Going back into Explorer, it now shows the same file that I deleted in Explorer - so it is re-saving the old file