So it's 2020, and I didn't actively know about comm(1):
The comm utility reads file1 and file2, which should be sorted lexically, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files.
So I now know that running tootctl accounts cull on my Mastodon instance in December listed 602 unreachable instances, this week there were 655, and 567 are in common between both.
Should be safe to purge those from the DB.
The social network of the future: No ads, no corporate surveillance, ethical design, and decentralization! Own your data with Mastodon!