This is now resolved. While looking up the properties files for information on uploading via curl[1], I noticed that the repository names didn’t match what was in the installation. I am unsure how this happened (maybe my incorrect steps or something else) but earlier we had repos set up as “snapshots”, “releases” and so on whereas the existing repos were “maven-releases”, “maven-snapshots”, etc. Upon adding back the repos as we had it and removing the new ones, the reconcile was able to reconstruct internal state. We’re now back to normal.
Regarding soft deleted content, the UI shows the blob to be 1.2TB and disk usage is 1.6TB. First course of action is to compact, then set up new cleanup policies.
Many thanks to Dawid Sawa and Matthew Piggott for their quick assistance.