Currently there are multiple places where some wikis are removed from all.dblist such as https://github.com/wikimedia/analytics-wmde-scripts/blob/9a4c17cd89000eb52c50ed5c50dbad92b7c8adf8/src/betafeatures/counts.php#L64
Per T126218#2009089 there is a dblist of these wikis (that are not replicated) so the scripts should just grab this list too and skip the wikis listed there.