Currently, --swapxy is never required and has been made a no-op, but --inverty is needed if you will re-import coordinates to cryoSPARC or if you have full cryoSPARC pipeline coords and you want to use them to extract in Relion on new Relion MotionCorr micrographs. You can check if they’re correct with disparticle.py or relion_display.
The way to reason out what you need is to remember that cryoSPARC imports coordinates from Relion correctly. So if you have a micrograph (in or out of CS) and coordinates in Relion, then import them, then export, you will need --inverty (in order to get the same exact values again). OTOH if you have coords picked in CS, to be used in Relion on the same micrograph file, then you don’t want any argument.
Since Relion/Motioncor2 flip the movie sum, if you are changing the actual micrograph file to one from a different motion correction, with those coords from cryoSPARC, then once again you want --inverty.
@user123 is right, check if your coordinates are correct and also if the normalization actually matters (very rare). Also consider if you have used a different box size or something else is different as well (SSD caching?).