What about using unionfs or overlayfs or something to combine a directory from both the SD card and the HDD? You could configure it so writes go to the SD card and reads come from both.
Then syncthing runs from the union and data data is added to the SD card. At night a cron job would sweep any new data from the SD card and put it in the HDD.
This would be tricky to get totally bulletproof if you want syncthing to be able to continue to be modifying files during that nightly cron job so you might want to pause it.