Batch conversion of .pdf to archivable document

I am replacing another employee, performing conversion of thousands of medical files to archivable format (sometimes singly, sometimes as batches).  I was wondering if Adobe programmers might be able to program Adobe to change the file type as read in Windows explorer when the file is converted.  The reason I ask is that there is no way to know when a document has already been converted without opening it. 

If performing individual file conversion, or it was converted previously, I must rename each individual file for reference.  Overwriting the original file is preferred to decrease steps.

When performing a batch conversion, the name is changed adding _A1b... to the end of the name, but the file extension remains *.pdf.  Batching also causes the file to be duplicated and requires individual deletion of each file. 

There has got to be a better way to see where I am in this process.  I am requesting that the file type be demonstrated in the extension ex: .pdfa... or a separate file started with the duplicates to prevent deletion of necessary files when removing originals.

Thanks,

Sarah