Possibility of syncing between Steam & GOG?

I have bought Starbound both on Steam and GOG, and primarily use the GOG version on my laptop so Steam does not use too many system resources in the background there, while using the Steam version on the desktop.
The desktop is far more powerful than the laptop, so it has no problems with the additional use of system resources by Steam's Overlay and Webhelper (among other Steam background-processes), but I made this move after the Steam version lagged on the laptop, whereas the GOG version does not.
Both systems run Linux.

Since there is no native sync option for Starbound to sync saves between different versions, I have created a simple bash script to transfer the files over;

Code:

rsync -rltDvu --inplace --append-verify -8 ~/.local/share/Steam/steamapps/common/Starbound/storage/ ~/bin/Games/GOG/Starbound/game/storage/

(Just the relevant bits shown. Omitted is the step where it transfers via a cloud server, as well as the reverse command.)

The main issue I have found is that, while it correctly transfers the SHIP and WORLD files, the PLAYER file seems to revert to an earlier state than the most recently saved. (Causing unwanted loss of progress, duplication of items, etc.)

Is there a way to do this at all in a way that may circumvent this loss of progress? Perhaps exclude certain files, or add additional file locations?

Any help with this would be appreciated.