My Syncthing Tray also provides a small CLI application called syncthingctl which can pause/un-pause individual folders.
Eg.
syncthingctl pause --dir docs-fh --dir docs-misc --dev martchus-server
will pause the directories docs-fh and docs-misc and the device martchus-server.
Of course it is also possible to resume. Internally it is using the approach @calmh described.
Due to the lack of documentation about this inconsistency I had to ask the same question when developing the tool just to be sure I didn’t miss anything.