Probably going to have to re-initialize the job master file and then reimport them (with the period removed).

Hopefully, you have not already created new jobs that are valid. If so, you will most likely have to manually removed the bad jobs with DFDM and then reimport.

We have been using the software. We just want to clean up the database now.

If you are unfamiliar with DFDM, I highly recommend you work with your Sage Partner. Deleting the wrong records could be ugly.

Renumbering jobs would be a tremendous undertaking. Depending on how you're using job cost, you may have payroll, A/P, S/O, and A/R files that reference job numbers. Renumbering every instance of the job number, in all of the transaction files in integrated modules would seem nearly impossible to me. Maybe not impossible, but it would take a lot of time and expertise in Visual Integrator and a thorough understanding of the Sage 100 data file structure.

I had the impression they had not been able to use the jobs since they were imported in which case that would be moot.

I wonder if doing a rebuild key files might strip out the bad job numbers? Couldn't hurt to try as long as you back up.