It's just a normal Ren'py engine game, there's no reason it should ever be flagged as a trojan. And other devs I asked have never heard of this happening before.
What antivirus are you using? And what files specifically got removed?
Norton and the .exe startup and some others i think.
I see. Well, it's a false positive. Talking to other devs they say it's likely because ren'py has the ability to connect to the internet to download game updates, so some anti-virus softwares will see that and immediately flag it until the game has been verified and approved by them.
I see all the time developers saying that a game's exe file is flagged as a trojan and to ignore it. Most AV programs are a joke. They find more false positives than they do actual viruses.