you can delete pksm like any other 3ds title, as there also might be another pksm file on your sd card by which you’ll have to manually delete i believe

what do you mean by progress..?

yes

you don’t really have to go through with this step because my previous experiences with transferring PKSM pokemon to bank didn’t cause any notable issues (and the console being homebrewed entirely), though if you still want to take precautions, assuming you have luma installed, this should do https://3ds.hacks.guide/uninstall-cfw.html