In the old days you took $10,000 to your bank or broker and got a bunch of certificates. Then, as coupons become due, you detached them from the bond (they were actual, paper coupons) took them to your bank and deposited them like checks. Then, when the bonds came due, you presented them to the bank for redemption. If you sold the bonds, workers in the bank's vault a/k/a the cage handled shipping certificates from the seller's bank to the buyer's.
But bearer bonds stopped being issued in the early 80s. Now, the issuer's transfer agent keeps an electronic registry of who owns what and who is due interest payments. When you sell bonds, the transfer is made electronically on the books. There should be very few bearer bonds still outstanding.
Also, they got wet, it's not like they went up in smoke. Bottom line, I wouldn't expect losses from destroyed certificates to be a big number like tens of billions. If they can't salvage them, sounds like it could impact some people, and could be a legal scramble to see who ends up on the hook between DTCC, the banks, the customers, and their insurance companies.