You need to restore the instances.json in the datastore by copying and renaming one of the instances.json-xxxx.bak files. Then from there run ampinstmgr fixperms in CMD and reboot.
The issue would’ve originally been caused by your CLI tools being v2.5, while your instances were on v2.6. Updating the ADS instance via the UI is bugged, but even if it worked that doesn’t update the CLI tools, as that needs to be done using a fresh MSI (AMP itself doesn’t have the permissions to do it).
From what you’ve said, you’ve probably indirectly updated the CLI tools, but you can check by running ampinstmgr version to see if it prints out v2.6.0.6.
Update guide for future reference:
https://discourse.cubecoders.com/t/how-to-update-amp-to-the-latest-version/2297