Safe mode disables most of BTT's functionality, including stuff that is very important for the hyper key, so that would not help with isolating the issue.
Did you use the standard hyper key setup? i.e. caps lock with the "act as hyperkey" action assigned? What kind of keyboard are you using?
How often did it stop working for you? If you can reproduce the issue, it would be great if you'd send me the logs from ~/Library/Application Support/BetterTouchTool/Logs (andreas@folivora.ai)
I do not see an option to make it work as a normal caps lock if hyper key isn’t used. I know there used to be one but after this new update, I do not see that.