One way to do this would be for decentralized 2nd layer apps to periodically (for example, once every 1000 blocks) generate a hash of their state (or some portion thereof) and publish it as a blockchain transaction.

2nd Layer Dapps should always broadcast a HIVE BlockID with their transactions imho. That way we know what block that specific dapp is synced up to. Also, to make it less demanding for dapps, they should be able to reuse the same HIVE BlockID for up to X amount of blocks.