It depends which program you're using, for example even tar will preserve hard links. Or on the other side something like duplicacy will just deduplicate everything that has the same content.
this post was submitted on 29 Nov 2023
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deduplicating is fine, the question is what it will do on a restore.
As far as I can tell from searching the web, duplicacy will restore two (or more) hard linked files as separate files. (Apart from the obvious one of losing the connection, your restore directory takes more space than the original).
Restic (again searching, but this I can probably test since I use restic) will restore them properly -- i.e., preserving the hard link
Why wouldn't you do a small test and find out before throwing literally everything at it?