I haven’t tried, but could the MySQL app be auto-suspending ? It doesn’t know it’s a database so it could be behaving like any other app and pauses when idle. Since it sounds like it worked when you deployed … but then moved to being suspended afterwards.
It’s not obvious but I think the default when creating a new app is to have it auto-stop when idle. That saves you money, but for a database you probably want it to stay running.
Check the fly.toml file (if there is one) and see if there is an option set in there to auto-stop. I think if no options are set, it should default to not auto-stop/suspend, but not sure on that.