I assume your handwritten checks are being entered as non-printing manual check batch entries, so you can enter the hand-written check number.
If you want to remove the incorrect check number, use Check Reconciliation to Reverse the check, then enter a new manual check (also non-printed) so that you can get the correct information. Reversing checks 'unpays' the invoices.
Do not do 'Cash Invoice' transaction types, as this is what prompts for GL accounts or distributions. Instead, use 'Payment' type checks, which can be applied to invoices.
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Regards,
Softrak Tech Support