That's very unlikely. GPOs are assigned 128-bit globally unique identifiers (GUIDs), and the probability of two different GPOs being created with the same GUID is astronomically small.
If Group Policy behaves inconsistently after a domain merger, the cause is much more likely to be Active Directory or SYSVOL replication problems, incomplete GPO migration, orphaned links, inconsistent DFS Replication (DFSR) state, or clients contacting different domain controllers that do not yet have the same policy data. DNS issues, site configuration problems, and lingering objects can also produce inconsistent results.
To troubleshoot, verify that the GPO GUIDs shown in GPMC are consistent across all domain controllers, confirm that the corresponding folders exist under SYSVOL\Policies, and check Active Directory and DFSR replication health using tools such as repadmin /replsummary, repadmin /showrepl, and dfsrdiag ReplicationState. Running gpresult /h on affected clients can also help determine which GPOs are actually being applied and whether clients are reading policy from different domain controllers.
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hth
Marcin