So uninstalling and reinstalling worked perfectly.

Confirmed that the weird self-conflict is a factor. I installed v0.0329_for_1.4.2 and clicked Refresh and Add available updates, then saw the empty changeset problem as reported. Then I restarted after manually editing my registry.json to remove the conflict of Scatterer with Scatterer, and now it's not empty:

(Not sure why the sunflare and config packages aren't listed there, since they're also checked for upgrade.)

The self-conflict was added in KSP-CKAN/NetKAN#4541, but there's no explanation other than fixing #1870, which has a discussion that seems to be outdated now about SVE-HighResolution including Scatterer somehow. Current StockVisualEnhancements recommends Scatterer itself with no funny business. I think maybe one of these had "provides": [ "Scatterer" ] at some point?

Maybe a solution would be ignoring self-conflicts on updates?
That feels a bit dirty though...

Well, first I'd like to get a better understanding of exactly how and why it breaks and whether this is in fact a recent problem. It's possible that this is highlighting some logic error deep within the relationship resolver, the fixing of which could improve general robustness. Or it's possible that the upgrade logic is tripping over itself somewhere along the line as it attempts to reconcile removing and installing the same identifier in one step.

Confirmed the speculation about provides: KSP-CKAN/NetKAN#4809, KSP-CKAN/NetKAN#5414

We probably can and should remove the self-conflict now, but preferably after fixing the problems it causes in the upgrade logic.

This exception is being caught:

And this is the content of that exception:

That's coming from here:

So it looks like a regression of the "Mods are allowed to conflict with themselves" behavior.

OK, it looks like what's happening is that SanityChecker is being asked to validate a hypothetical situation in which updates are installed without removing the old versions. And it always worked that way, but prior to #2339, the exception was avoided because conflicts were done only in terms of identifiers without regard to versions, so the old version of a mod was always considered not to conflict with the newer version simply because their identifiers were the same. We have Scatterer 1 and Scatterer 2 sitting next to each other, and now our "self conflict" check is version-specific, so they are counted as conflicting with one another (but not themselves). This loop skipped "ourselves" as it said, but also other versions of ourselves!:

In effect, the weirdness of this aspect of upgrading was masked by #2325, and fixing that issue brought it forward. I see two ways to fix it:

1. Make the equivalent logic in SanityChecker work only based on identifiers again, so a mod list with multiple versions of the same mod would be considered consistent; or
2. Revise the upgrade logic to prepare a more complete hypothetical scenario in which the old versions are removed before passing to SanityChecker

The first option would be simpler and safer, but the second would be cleaner in terms of how it "should" work.

It sounds like we need a more robust model of a "change" that involves "(remove [a,b,c,..]) and (add [x,y,x,...])" and stop trying to consider "upgrade" as a unique change type.

Experienced as reported in first post. Only seen this concerning the mods "Scatterer" and "VesselMover Continued".

Thanks @Sunesha, VesselMoverContinued fits the profile in this issue (conflicts with itself, but via a provides property rather than directly), and it seems to be fixed by the change in #2430.