[Pro] Upload stopped. ( 5.3.2 )

I upgraded to 5.3.2 a few days ago, and I started having a problem I never had with 5.1.1.

I cannot Upload the site without Resampling All Resources.
If I don’t, one of the .swf files I embedded on pages will appear as to to be NOT FOUND,
and stops the upload. “Cannot complete upload because file not found.”
It is always one of 3 .swf files out of the total 7.

The files in the Site folder had never been moved or modified in any way.
The Flash documents had been saved in the Site folder to begin with, and the .swf had been published
by default in the Site folder. Updating that particular “unfound” .swf doesn’t work either, because another one pops up during the upload.

Again, never had this problem with the previous version.

I would be really grateful for a solution, as I am not able to find one myself.

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