I thought the file conversion was across the board of modules, so Douglas you were initially correct about the orphan batch files; thank you.

From within the company Data Set I was able to remove the orphan batch files since Pete was able to help me identify them (I noticed the date modified on the files were old as well).

So I went through the following process:
Restored from backup,
Removed the orphan files
Did a Data Integrity (which was error free)
Created New Batches

End Result: Number sequence was correct.

Issue Resolved. . .

Thank you very much everyone!