Is there a way to take one file in a multi-file document and upgrade it to a separate object with its own class?

They should be able to select the file and copy (Ctrl+C), then paste (Ctrl+V). This will start creating a new document with the file. Afterwards they can delete the duplicate file from the original multi-file document.

Thanks Joonas Linkola , the pop up screen with the notification about the potential duplicate was opening in another screen and I did not see it.

I'd rather go for separate classes like transmittal and Project Documents. Every document gets saved to project documents class with it's own metadata. When that document is sent or recieved, in metadata, I'd mark it in "related outgoing transmittal" or "related incoming transmittal" multi-select list. 

So, every document would have their own metadata even there are multiple different documents in one batch. The documents will also have relation to transmittals which would have transmittal related metadata (date, who did you send those, other details).

Thanks CagriE .  That is our existing method but, some users are asking for easier options - put everyhing in a box and click send.  I guess pros and cons on both, I guess it is good to have options and let the teams decide if they would like to make things easier for end users and then spend a bit more time in the back office organising documents.