Add an "error" account, put transactions there so that your transaction accounts have the correct value, and focus on inputting current data.
If for some reason you care about your historical data enough to import it, you can add new transactions into "error" to subtract whatever part of it they are responsible for. If the account reaches zero, you can even cheat and delete all transactions.
GnuCash actually does that after an import. Sure, one can use the nice reconcile flow, but for importing lots of data I prefer slowly working through the bank statement at my own place, paired with occasional sanity checks.
Comments
Add an "error" account, put transactions there so that your transaction accounts have the correct value, and focus on inputting current data.
If for some reason you care about your historical data enough to import it, you can add new transactions into "error" to subtract whatever part of it they are responsible for. If the account reaches zero, you can even cheat and delete all transactions.
GnuCash actually does that after an import. Sure, one can use the nice reconcile flow, but for importing lots of data I prefer slowly working through the bank statement at my own place, paired with occasional sanity checks.