Ran across this error today too:"Relation and/or reference table" <table name> "is not a known CI Type" .   The fix was to 'rekey' the mid server (select MID server, then select Rekey from drop down choice list).  After "Re-Keying the MID" the Discovery job & Pattern worked as expected.   An odd error, don't know what caused it to begin failing.... but the "rekey" option worked!