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We have tables that are brought in using metadata loaders. The tables have been deleted in the database but the pages remain in Connect. Is there some kind of auto archive process that will archive tables if the page for the table is in Connect but the table is missing from the metadata loader?
deleted tables from database should be also "marked as deleted" and not visible in Connect after next metadata loader run.
We may need more information like which version of Connect you are using, if you have any annotations on objects in Connect and also if you see any error messages in your Connect log from your recent metadata run.