JPEXS Free Flash Decompiler Issue Tracker

Do you mean Save as EXE functionality? Adobe discontinued Flash Active X feature on newer Windows so "Wrapper executable file" EXE export won't work in such case. You can create "Windows projector file" instead by selecting it from file type dropdown when selecting output EXE path. You will need to download the windows projector somewhere on the interwebz and set its path in Advanced settings for it to work correctly.

Interesting that even with discontinuation, the original file is an exe-type flash that works, I thought that saving it in the same format should work too, but I'll try to find a projector. Thanks.

No, the EXE file we open can be literally anything - a game or EXE with any structure, that just contains SWF as a part of it. Then FFDec loads it. You cannot expect FFDec to save SWF to the same EXE as it was loaded from, because FFDec does not know the structure of original EXE and how SWF should be stored there. Save as EXE feature in FFDec is more like "Export AS EXE" - ignores the source EXE it was loaded from and creates EXE with new structure based on FFDec stub (Wrapper - Active X) or projector stub. I am closing this.