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A SQLite database can be rebuild (and therefor optimized and defragmented) with the VACUUM SQL statement.
Executing this statement requires that you cannot really work with your usual database components.
A little trick that does the job:
uses sqlite3ds;
...
var dbVacuum : TSqlite3Dataset;
...
Connection.Close; // your TSQL3Connection
dbVacuum := TSqlite3Dataset.Create(nil);
dbVacuum.FileName:=Connection.DatabaseName;
dbVacuum.ExecSQL('VACUUM;');
dbVacuum.Free;
Connection.Open;
...
