I used to edit a website a while back and experienced some of the same issues. It was with an older version of Flashfxp, but for some reason when I would save the file by over writing the old one, I'd get the errors.
What I found to be a good work around was after downloading and doing the editing I needed, I would save the file under a different name, i.e. if you were editing flash.idx, I'd save the new one as flash1.idx. I'd then reupload it and once I had it the way I wanted, I'd delete the original and rename the edited one to whatever I needed it to be.
I can't tell you why it happens, but this way worked for me.... Hope it helps you out.
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* FlashFXP v4.1.8 build 1708 BETA. registered
* Windows 7 Ultimate x86
* ESET Smart Security 5.0.95
* Cable Network
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