Recently I have updated one of our custom tabs in the Safety Report module by creating a duplicate, making my changes and then disabling the old version and enabling the updated one.
The report includes some conditional formatting that shows or hides tabs based on various selections by the user. By putting in place the updated version I broke those formatting options because they were still referencing the old (disabled) version.
A way I could've avoided this would've been to make the changes in the current version instead of the new one, but sometimes it's easier to take some time in preparing a new version and putting it in effect when ready.
My suggestion would be to implement a conditional formatting error check that verifies whether the current conditional formatting is referencing tabs that are actually enabled and will display an alert if that isn't the case.