What exactly did `Bitcoin-Qt -rescan -reindex` do?
-rescan likely did nothing at all. It goes through the blockchain to find transactions that are missing from your wallet. It is only very rarely needed (like when you manually changed things in wallet.dat).

-reindex throws away the block chain index and chain state (the database of all unspent transaction outputs), and rebuilds those from scratch. It is exactly like downloading the block chain again from peers, except the blocks already on disk are used.