It would be a good idea to point out that the developers of Checkpoint
don't like SXOS and, to that end, made design choices that had the effect of making it unusuable on SXOS.
As of Checkpoint 3.2.0 it no longer would work properly on SXOS, only allowing the first 20 games to be backed up. As of 3.2.4 controller input was unresponsive entirely. As of 3.5.0 it caused system crashes. Using older versions of Checkpoint worked until around 9.x after which point Checkpoint ceases to be a viable option. Anyone who was relying on Checkpoint will have already encountered problems and risk loss of everything if they continue to use Checkpoint.
This is concerning because, rather than forcing everyone to use Atmosphere like they appear to want, it just fractured the save backup scene. Now SXOS has it's own "SX Save Manager" which will go it's direction while Checkpoint will go in a different direction entirely. That means we'll soon see incompatibility in save editors and an impossibility in migrating from one OS to the other - so even if someone wanted to switch to Atmosphere they probably won't be able to anymore. Unless, of course, either Checkpoint or SX decides to support the saves of the other group.
Regardless of how anyone feels about one OS or another, that's not a good development. Combine with the fact that Checkpoint appears to have stopped development entirely and it's going to be even worse.
As a side note, I'm curious: To those of you who are capable of using both SX Save Manager and Checkpoint, are the saves interchangeable at this point at least?
Yes, unfortunately, that will never be fixed. I reported that issue as an SXOS user and they blamed SXOS rather than considering that it may have been a problem with their software. It doesn't surprise me that atmosphere users are affected.
For SXOS users with this issue: If you have a backup of an emuNAND older than 9x and can find a version of Checkpoint older than 3.2.0 you should be able to restore your saves that way and then could use SX Save Manager to create new backups that will work on the latest firmware.
Unfortunately, since you can't restore games via Checkpoint that didn't already create a save you won't be able to use this trick on any game that doesn't work on Switch FW 8.x
I like to create a backup of my emuNAND every time I update and I save those backups so I can roll back if I ever need to.
If you are on SXOS, don't bother. It no longer works. When it did work, however, you would have gone to Homebrew Launcher and selected the NSP and then open it. No install required.
and that was the beginning of the end for Checkpoint...
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