When you have Historization enabled, this is not what you should be seeing. No records are lost from the GH table. When two golden records are merged, the one with the 'losing' ID remains in the table. 

What you should see against this row is the B_TOBATCHID column now has a value. It's like a history record, not with an 'end date' but with a 'To Batch'. The 'From Batch' to 'To Batch' indicate between which Integration Batches that record existed as its own golden id.

Try ordering the GH table by the id column and you'll see that it is still there.