I have no idea why Checkpoint would give you an SMDH file, especially not one of a completely different game. If restoring your backup works without any problems you might have copied the wrong file from your SD card.
Make sure you got the file from /3ds/Checkpoint/saves/IPGE POKEMON SS/<date-string>/POKEMON SS.sav
If that file is really the SMDH try making a new backup by follwoing this tutorial and use the latest version of Checkpoint, which is 3.7.4 as of now https://github.com/FlagBrew/Checkpoint/releases/tag/v3.7.4
Or try using TWL Save Tool instead.