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Remember that Oracle GoldenGate supports the Oracle TRUNCATE TABLE command without enabling DDL(using GETTRUNCATES), but not TRUNCATE PARTITION. You can replicate TRUNCATE PARTITION as part of the full Oracle GoldenGate DDL replication support.
Assuming you have DDL replication enabled, disable the DDL replication and then truncate the 3000 partitions. Once done, enable the DDL replication again.
If you know the names of the partitions you do not want to replicate, you can try with DDL EXCLUDE. e.g. The below should include all DDL for replication except the truncates of partitions p1
DDL INCLUDE ALL EXCLUDE INSTR ‘ ALTER TABLE FACT.ORDER TRUNCATE PARTITION P1'.
you can try with wildcard for the partition names if they have names containing same characters. Go through oracle documentation on DDL exlude.