The database wasn't renamed (ie pa_uswikimedia), just the server side links.

Still in the same database lists:

reedy@fenari:/home/wikipedia/common$ grep pa_uswikimedia *.dblist
all.dblist:pa_uswikimedia
closed.dblist:pa_uswikimedia
s3.dblist:pa_uswikimedia
small.dblist:pa_uswikimedia
wikimedia.dblist:pa_uswikimedia

https://meta.wikimedia.org/w/api.php?action=sitematrix

<special url="http://pa-us.wikimedia.org" dbname="pa_uswikimedia" code="pa-uswikimedia" closed="" />

^ I wonder if that "code" changed..

Is this still an issue?

Can you post the proper error messages you get when you try and re-add it.

Might need to temporarily give myself rights to test the changes to the wikisets...

Quite simple, it says:
The following wiki does not exist: pa_uswikimedia.

This just happened again with wikimania2012wiki.

"The following wikis do not exist: ukwikimedia, wikimania2013wiki."
It was necessary to remove them before any other wikiset changes could be made.

This error is shown if there is a wiki in the input not found in the centralauth wiki list.

	function wmfCentralAuthWikiList( &$list ) {
		global $wgLocalDatabases, $IP, $wgSiteMatrixPrivateSites,
			$wgSiteMatrixFishbowlSites, $wgSiteMatrixClosedSites;

		$list = array_diff(
			$wgLocalDatabases,
			$wgSiteMatrixPrivateSites,
			$wgSiteMatrixFishbowlSites,
			$wgSiteMatrixClosedSites,
			MWWikiversions::readDbListFile( getRealmSpecificFilename( "$IP/../nonglobal.dblist" ) )
		);
		return false;
	}

	$wgHooks['CentralAuthWikiList'][] = 'wmfCentralAuthWikiList';

This doesn't seem right. Why are closed wikis not considered as CentralAuth wikis?

Looks like GlobalUserPage also uses this list for the cache update job.

Does CentralAuth make use of this list anywhere else?

In T48746#1465034, @Glaisher wrote:

Does CentralAuth make use of this list anywhere else?

I took a look around while waiting for my flight home. Starting from CentralAuthUser:

• getWikiList
  • validateList
    • adminUnattach
  • importLocalNames
    • lazyImportLocalNames
      • listUnattached
      • addLocalName
        • CentralAuthPlugin::initUser
        • CentralAuthHooks::onAddNewAccount
        • CentralAuthHooks:onRenameUserComplete
      • removeLocalName
        • CentralAuthHooks::onRenameUserComplete
        • CentralAuthHooks::onDeleteAccount
  • SecurePoll extension
  • WikiGrok extension

In T48746#1465030, @Glaisher wrote:

Looks like GlobalUserPage also uses this list for the cache update job.

Our config does $wgHooks['GlobalUserPageWikis'][] = 'wmfCentralAuthWikiList';, yes

That probably means we actually depend on it to not include closed wikis... Perhaps we can just simply use $wgLocalDatabases on Special:WikiSets? But this would mean that, it would be possible to add non-CentralAuth wikis to the wikisets without actually having any effect. Is doing that a bad idea?