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For having the BSQ and the BTC wallet keys on different BIP 44 paths we added support for BIP 44 which was only partly supported in BitcoinJ.
We use the same seed words for both BTC and BSQ wallet but we store the wallets in differnet files.
I reviewed BIP44 implementation on bisq.
Bisq's BIP44 support
Minor issues found
BIP44 in bitcoinj
bitcoinj release status
Reviewed bisq code
Reviewed bitcoinj commits/PR/issues