Got similiar Problem using 2021.3 LTS. I was adding some Text-Mesh Pro Text to the Prefab when it broke. Undo function right after it broke did not undo the issue.
Just with the original post I get 3 duplicate entries named. I did run into this problem 2 years ago as well. At that time I could find the numbers in the broken prefab, I think from that I could figure out which sub-element caused the issue, I changed the ID of the sub elements, embeded them in the broken prefab and it worked.
Now, I cannot find the IDs called out in the error message in the prefab.
The Bi-Section approach proposed above, probably works but it will take me 16+ iterations to find the line in question since my file has a lot of lines.
The ID listed in the error message ist not the instance ID it is the “local identifier in file”.
This post how to search for game objects based on the local identifier. I will try to make it into an editor script.