Checking the provided scene files, we detected a corruption in the content of the ancestor scene, where the prefab instance pointing to "8883655615442723683" has a duplicate property "m_AnchoredPosition.x".
File: RampVr_01-04_Crew_Stairs.ancestor.unity
Lines: 9560-9569
For this reason, even though the source and destination scenes have solid information, the merging calculation against the ancestor scene fails.
Removing the duplicate property from the ancestor scene makes the merge operation run properly.