If you made manual changes to the invoices after they were imported in Accoutning system. For example if you change the amount of the invoice directly in fortnox, or if you void it without making the corresponding change to the correcting voucher, you have to correct this otherwise you will get diffrences between they systems, and revenue and VAT will be incorrect in accounting.
You changed amount of an invoice directly in fortnox
You need to find the correcting voucher and change the amount so revenue and VAT has the same amount as on the invoice and that Sales Ledger account has the same amount as the total amount of the invoice.
When the payment is later imported to Nitesoft the invoice in Nitesoft will become overpaid or underpaid, see article on how to fix that here.
You voided or credited an invoice directly in fortnox
You need to find the correcting voucher for the invoice and remove all transactions on this voucher.