With the proprietary web based accounting software 'e-boekhouden.nl' (and probably others), you can make specific rules into what ledger an entry from an imported bank account has to be placed.

For instance, I can tell the import matcher to automatically put a payment with the number 4010 into the ledger with number 4010.
Or filter on specific words: 'Contribution' goes to the ledger '8100 Contributions'. And so on.

With this approach, I have almost 100% certainty that a payment is associated with the right ledger.

With GnuCash (version 4.13) many payments go to the wrong ledger. Especially with a large amount of entries, there is a lot of manual work needed to correct this.