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When searching concatenated databases, Concordance Desktop searches across all concatenated databases but because it searches each dictionary file one by one, searches may take a bit longer.
Saving queries executed on concatenated databases is the same process as saving them when reviewing one database at a time. All searches from all databases in the concatenated set are saved. Query files are stored in a .qry file, and can be restored on a concatenated set as you would a single database. You just need the databases to be joined when you save the query and when you re-run the query. Re-running the queries on a concatenated database set gathers any updates made since the last time any database was reindexed.