I have a similar issue and so did a little digging using queries against tooling API.
The packages I couldn't update or delete were listed in the tooling API
SELECT Id, Name, SubscriberPackageID FROM Package2

The SubscriberPackageID is supposed to refer to the Id of the MetadataPackage record in your org. It was here that I could find no entry for the packages.
SELECT Id, Name, PackageCategory FROM MetadataPackage

I have raised a case with Salesforce. One consideration is that We have had an instance move since those packages were created and seem to be no longer accessible.
===Update===
After raising a Case, have had the following back from Salesforce
I got an update on the case from the senior Tier-3 team that it has been identified as a bug. The team is working on the fix and will try to deploy the fix as soon as possible. Though there is no ETA for the same but might be deployed as a patch in an upcoming release. We can also provide you the bug id i.e, W-8864667 for future reference on the fix of this issue.
see Known Issue - https://trailblazer.salesforce.com/issues_view?id=a1p4V0000003yQoQAI