Which version/build of FlashFXP are you using?
The latest release v1.4 build 830 should correctly prompt you to save a file on exist.
FlashFXP does not restrict external applications from writing to a file that is currently being uploaded.
And here is why, In some cases the file may be open by another application for read/write which will prevent FlashFXP from opening the file for read access + deny write.
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