I encountered a problem with one game : "Minecraft - Nintendo Switch Edition" (not Bedrock edition for Switch, haven't tried that with checkpoint yet)
I backed up my save on an SXOS emuNAND using checkpoint, created a new emuNAND, and then restored the save using checkpoint.
The problem : While the worlds did restore with all block positions, all items in all chests in the world were empty - whether created by me or part of a dungeon. All villagers were gone (which is the first thing I noticed because I had a people zoo). All worn equipment was gone, but items in inventory that wasn't worn was still present.
I have the original emuNAND backed up so I could try using checkpoint on it again later if this problem is fixed.
EDIT: This problem is not present in the bedrock edition for Nintendo Switch, but it would suck to have to use that version. I went back into the old emuNAND, opened the Bedrock edition, selected to sync old world (to import from the Nintendo Switch edition) and then used checkpoint to backup the bedrock edition. Then I went back to the new emuNAND, restored from checkpoint, and all the items appear to be present in all chests. Of note, however, is that after restoring the save file is around 10 MB less, so some data must be lost somewhere, just don't know what's different yet.