opening the GUI on the raspberry pi while it’s busy doing anything else is a bad idea because it causes additional CPU load.
You probably have this problem: https://github.com/syncthing/syncthing/issues/1751 increase “pingTimeoutS” in the advanced options
Another thing you can try is running http://build.syncthing.net/job/syncthing-bolt/ on your RPI, this also fixed the issue for me without increasing timeout