Manual recovery problems may occur during recovery of a primary database.
A new generation ID for the primary database has not been set. See Replication Server Administration Guide Volume 2.
If you loaded the primary and replicate databases from the same backup, make sure the rs_lastcommit table for the replicate database has the correct entries. If the origin_qid in the rs_lastcommit table is incorrect (old or changed), the Data Server Interface (DSI) may ignore certain transactions associated with that origin_qid. Use bcp out to copy data from the rs_lastcommit table, load the data, and then copy the data back to rs_lastcommit using bcp in. If DSI still ignores certain transactions, update the origin_qid value to 0 to force DSI to accept these transactions.
If you used dump and load to synchronize the primary and replicate databases because of a failure, increase the generation number in the primary database. If you do not correctly set the generation number, replication from this database may stop because Replication Server perceives that it has already processed the messages.
See Replication Server Administration Guide Volume 2 for information about recovering primary databases.