Very odd.

I had no problems after buying this when it was on offer.

+1 to you for coming back with the fix, so it will help others with the same problem

Very odd indeed. I don't really see how the patch can delete your FTL.executable, unless either your downloaded patch was faulty (redownload) or, what I think is much more likely: Are you running an antivirus program beyond the MS Essentials in the background?

Its really not easy to completely get rid of antivirus, I'm guessing it somehow quarantined the executable anyway. Might be logged somewhere.

btw...a new patch was announced on the official forum, so it will probably show up here soon.

I redownloaded it with the same result and am running no other anti-virus apart from MS Essentials, which I turned off
I also restarted the computer, but to no avail

considering that it deleted itself, I also figured it had to do with anti-virus, since that's usually what happens if it doesn't like a file - but I could not spot it anywhere in the history of my AV, hence I was even more stumped

should also be noted that I'm running Windows 7 x64 (always a good thing to add at the very least the OS in cases like these, so my bad)

also after I had patched it (before I figured out "the fix" ), the .exe file would have the exact same size as the un-patched one, hence I'm thinking that there might have been some kind of delay/mishap during the patching process and that this somehow triggered once I tried to activate the .exe file itself

i.e. the patching told me it was done, when in reality it had not finished and thus upon executing the file it would "continue" the patching process, thus removing said file
(far-fetched, I know - but I'm trying to find a logic reason for what happened)

hopefully this will help others, should they ever encounter the same issue

either way it was a great purchase and I have not lost any faith whatsoever in either GOG, nor the makers of FTL due to this minor issue