This isn't the kind of thing that would change on its own, though I can't explain how it appears as though it has changed on its own. You could check Admin logs etc. to see if it has been done by error.
It would be a case of doing it one by one, unfortunately.
It's worth noting, however, that those being on "Inherit" may well not be a problem.
Look at this for example:
I have set "Main Forum" to be Private, but then added permissions that only allow "View node". However, I can still "View threads by others" etc. as these are inherited from my global user group permissions.
Before making any changes, I would look at using the Analyze Permissions function to verify the users have indeed lost access to those forums. They may not have, or it may be another permission not directly related to the node itself that has changed,