I've used a file deduplicator on a large folder with hundreds of thousands of files. The deduplicator created hardlinks for all duplicate files that it detected.
If I was to attempt to merge some directories that contain some hardlinks to the same files and allowed overwriting of the targets I expect that file corruption is possible.
In my case the filesystem is ZFS with a 3.14 kernel.
I don't want to accept what happens based on empirical evidence from the case of a test involving a few files. I want to know exactly the process involved to know if there is a risk of file corruption for various reasons like power interruption, or other unsolicited interruption.