Bitcoin Core HD Wallet v0.13.2 missing confirmed incoming transaction
Bitcoin Core currently has no internal function to recover a complete wallet. If the key is unknown (not generated yet), Bitcoin-Core will not detect transaction from to to that key/address. Also, the keypool size does not matter at this point, funds sent to a keypool key/address are not detected at the moment.

For now (Bitcoin Core &lt;= 0.14.0), if you restore a backup, make sure you generate plenty of addresses, loop through getnewaddress and ensure you generate 1000 (or more?) keys.

After you did this, restart Bitcoin Core (qt/d) with -rescan

Hopefully we can add some HD restore features for Core 0.15.