I mistakenly upgraded all of my files from 9.8 to 13.1. Having a problem with some files being recognized by software

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I mistakenly upgraded all of my files from 9.8 to 13.1. In the process, a number of files could not be "renamed" and thus did not upgrade. I am unable to access job cost records and unable to process payments in Accounts Payable. The File Doctor report mentions using the Windows file tool to rename the problem files and then to try upgrading again. Has anyone else experienced this kind of problem?