There are several ways in dealing with it in your case.
You can simply turn off the enforced Check in/out mandate, then you need not bother yourself.
If you are run MOSS then you many resort to 'manage structure and content'. I got this suggestion couple of weeks ago yet have not used it. It seems little bit complicated process. Hope you can do it.
If you are in complicated situation, then you need some tools like Sharepoint Batch Check In