That's a really good question. I guess code specifically wouldn't be copyrighted after that time and wouldn't have any value in its physical format. I'm also not sure how hard it is to track property ownership over 1000 years, or if it applies between governments. Ancient artifacts whose ownership is in question could be legislated to not transfer ownership to the discoverer; that's not really burdensome. There's also laws regarding abandoned property. If e.g. Stallman was buried with printouts of emacs and a tomb robber steals the copy, the entire chain of transactions is tainted from that point on.

But as painful as it would be to lose it, if you had verifiable proof that the documents the code is printed on were legally yours, you shouldn't be obligated by outside parties to handle them in any particular way.