In an effort to speed up some processes, we wish to move most of the old custom datasync export files from their current location to a new directory. Are there any negative implications in doing so?
There are no negative implications in moving these files. All old custom datasync export files could be archived in a new directory within or outside your designated FTP location.
If you choose to keep the archive within your designated FTP location, note that at some point you would run out of your FTP quota and you would be advised to move or delete some of those archived files to create the needed space for your custom datasync to run optimally.