It's not that the database ID has changed, as the recommendations are done by database name. Every few minutes, SQL Response checks the SQL Server error log, and if it finds a ^DBCC CHECK(DB|ALLOC) \\((.*)\\) \\w, it updates the DbIntegrityChecks table in the alert repository. SQL Response then checks this table for changes every five hours.
I suppose you could query the alert repository tables using sqlite3. It may be quicker to delete the alert repository files and start over, though, if the problem is corrupt data.