Hey,
this seems like it is not a Syncthing error since it appears that the inotify handles are just not set permanently. This is not the right forum to fix this error. Try it at a Synology forum.
For configuring anything to always happen automatically, particularly to survive a DSM upgrade, always use the Task Scheduler. Any other method will eventually be over-written.
I have it run a script that, amongst other things, runs on boot sysctl -p /volume1/<path>/sysctl.conf where sysctl.conf contains fs.inotify.max_user_watches = 204800