This is more hand-waiving than actual help, but here are a couple of ideas.
First, now that you know what index is broken, you can reindex just that one and not every index in the database. You might ask https://ask.discourse.com/ for a hint for how to do that.
Corrupt indexes in PG12, how do I fix? - #11 by sam also has some hints.
Since you don’t care that much about this link tracking (and I guess a new one has been created anyway), just deleting the duplicates is fine.
There should be a way to do a query that will find the duplicates so you could delete them all at once.