The first thing to say is that there is no need to change anything about these files. Word 2016 can open DOC format files.
'Compatibilty Mode' is not an error message it is merely an indication that the current file was created with an earlier version of Word. Updating such files can alter their appearance, not always beneficially. I can't think of any good reason to change them.
That said check whether the files in question are flagged as read only and whether you have write permission to write to the folder where you propose saving them.
You may find
http://www.gmayor.com/document_batch_processes.htm useful