During a merge, Amazon uses a hierarchical catalog logic based on data trustworthiness and performance history.
Typically:
The ASIN with higher traffic, conversion rate, and review volume becomes the survivor.
Its identifiers (including GTIN) often carry forward, unless you explicitly state in the ticket that the GS1 barcode is the valid one.
So, attaching proof of your GS1 certificate increases the odds of the GS1 identifier being retained as the master.