Check with your Sage partner as there's a  widely used utility that allows them to copy/paste all your PDF files and then run a utility to point Sage to the new location. It's a huge timesaver.

Are you referring to the Link Maintenance Utility in Library Master? I used that for some of the smaller directories with PDF files, but the invoice PDF directory originally had 267,000+ files. When I was using the Link Maintenance Utility to move files, it errored out when there were a great number of files (I can't remember how many exactly). 

Right now I'm using the Customer Viewer as I'm trying to switch from one large directory with hundreds of thousands of PDFs, to separating them out by year. I'm also cleaning up the directory by removing any links that don't have an associated PDF.

I believe Wayne is referring to a custom (internal) utility available to members of 90Minds.  It has no such problems (as you describe).

They might want to make use of the Purge PDF Documents utility in Sage 100.  See "Purge PDF Documents from the System" in Sage 100 Help.

Okay I'm not a member of this organization so I have no access to this utility.

I would go to their web page and reach out to them.  The member who created it probably makes it available for a nominal fee.

I already completed the task so it's a moot point.