I don't have a website with GoDaddy and I don't intend to pay them for the privilege of looking into this (AFAIK they don't offer free web services). If they won't tell you anything at all, then my hands are tied. I appreciate the offer to poke your FTP, but seeing the file be automatically removed won't really tell me anything.
As far as stripping things out. If an essentially empty project is triggering their security machinery, then there's not much you'll be able to do. Certainly, it's unlikely that stripping out parts of your project would make a difference.
It's likely going to end up being a false positive from a poorly written heuristic rule from some AV/M suite. I'll submit an empty project to VirusTotal later to check on that front.
EDIT: Well, apparently the current virus database from ClamAV thinks it contains some Microsoft Edge-specific vulnerability exploit. I've submitted a false positive report. We'll see where that goes I guess.
With no other information to go on at the moment, I'm going to assume the ClamAV complaint is what's up GoDaddy's idiotic arse.
EDIT x2: If anyone has ClamAV installed, could you please check projects compiled against recent versions of SugarCube v2 (even empty projects will do). As noted in my last edit, I've already submitted a false positive report, but I'd like an independent confirmation if possible (in case they want to play football). Right now I'm relying entirely upon VirusTotal's report.