Remote Backup Issue

Here is a summary of the past few months of owning my two WD My Cloud systems:

-Have been using remote backup feature sucessfully between two identical My Cloud EX4100s at different houses for a few months
-Placed 4TB of files on main system
-Physically brought over backup system and manually copied new files to it
-Both machines are now identical
-Remote Backup feature won’t detect manually copied files and tries to overwrite manually copied data
-Cannot transfer that many files again over internet, too slow and other various problems

How can I make the WD My Cloud EX4100s recognise the manually copied files in the backup, is there a way of doing something like manually editing the backup logs of something? I desperately NEED a solution to this. I contacted WD Support and they couldn’t help. In summary - I need the main systemm to know that the other system already has the files and it should skip them and complete the rest of the backup. Thanks for any help in advance!