...the timer will remain enabled but no UI element will be present saying this was manually done. Either the UI element needs to stay, or the timer needs to be returned to it's previous state, although that might not be a good idea because some other bundle could have enabled timer changes since then.
The reason it disappears right now is because it will disappear on run change, as I'm not sure how else to handle it. This doesn't cause any other bugs, it's just a confusing UI one, so not urgent.
If timer changes have been disabled and then...
...the timer will remain enabled but no UI element will be present saying this was manually done. Either the UI element needs to stay, or the timer needs to be returned to it's previous state, although that might not be a good idea because some other bundle could have enabled timer changes since then.
The reason it disappears right now is because it will disappear on run change, as I'm not sure how else to handle it. This doesn't cause any other bugs, it's just a confusing UI one, so not urgent.