The solution is;
- Open Discover and Install Flatseal by searching for
flatseal
in the search box - Once installed, launch flatseal
- On the left scroll down until you find “Syncthing GTK” and click on that.
- On the right scroll down to the “Filesystem” section
- In Other Files click the button on the right with a picture of a folder with a + plus sign
- Type
~/.var/app:rw
- Close flatseal and restart the Steam Deck (or find a way to restart sync thing, I tried via the web interface and systemctl, and nothing changed but restarting the Steam Deck worked the best).
Then it should work to sync folders inside of ~/.var/app
.