It seems not to be an isolated case: http://monkeycoder.co.nz/forums/topic/prebuild-exe-file-missing/
I wonder if it might be worth running the itch.io releases through something like VirusTotal so as to give a wider view of virus test results for peace of mind. (You’d link to the results page, like I’ve done below.)
You can see some VirusTotal output results linked from here (some simple GTA V mods I wrote):
http://hi-toro.com/gtbunnymods/
(These mods will be no use on current GTA V versions, by the way, though source is included for anyone interested!)
Usually, you’ll get 1 or 2 false positives for almost any file, but when only 2 of 55 virus test results give “gen*” (generic) results, it’s pretty easy to see that a file’s safe.
I’ve only ever uploaded one file at a time (zip in this case), so haven’t ever used the API for uploading thousands of files like you’d probably have to do for Monkey2 (though possibly it updates the hashes for all executables in an archive?) — might be worth a look anyway.
I imagine it would be slow as f’ though!