Syncing a shared data partition, across two dual boot systems?

I have used Inscync in the past for syncing files across my desktop and laptop, both of which share a NTFS data partition, dual booting windows 10 and Ubuntu. I know that sometimes in the past, depending on the order in which I set up Insync across the 4 different operating system installs, duplicates sometimes have occurred, and I have had to start from the beginning.

As I am syncing my eclipse_workspace this takes some time, and I would rather not have to redo any of the syncs. Can you please tell me if you have any tips to avoid the duplicates?

At the moment my plan is this:

  1. Backup the files to sync locally on some drive.

  2. Not have Insync connected to any account on any OS.

  3. Delete everything from drive.google.com manually.

  4. Point Insync on Ubuntu on my desktop at the files I want backed up, then do the same on windows on the same desktop (pointed at the same files on the same shared data partition) (where Insync should just check the files and not download or upload anything) - this is where I think duplicates have occurred in the past.

  5. On Ubuntu on the laptop use Insync to download the files from Google Drive to the shared data partition, then on Windows on the same laptop point Insync at the same files on the same shared data partition (where Insync should just check the files and not download or upload anything).

Any tips to avoid duplicates, or is there a better method to do this?