I have zero inside info about how things work. Someone may reply with the definitive answer but I would try a few things while waiting. The every two or three days sounds suspicious. Is the projected boosted? I would maybe try creating another project to make sure it works without incident. Then move the code you have to that one.
That won’t explain the issue you’re having of course but maybe it goes away since it doesn’t sound “normal”.
There were some posts about enable-pnpm. I don’t know if that might help and I typically don’t like setting things without some idea of the impact. I have a discord bot running, I’ve updated it frequently and it hasn’t behaved odd except for the occasional bug I might introduce.
BTW, I’ve taken to not editing on the Glitch site except perhaps as a hotfix. Much preferring to work on my PC, push to GitHub and then release to Glitch. I find it works flawlessly and I know where the latest code is.