Negative stock should not be allowed in case of perpetual inventory, as we do not know purchase cost of those item at the time of delivery. We will add a validation for that. But till the validation added you can follow a trick, if you post manufacture entry on a previous date than delivery date system will book accountung entry for the delivery.
And to sync stock and account balqnce manually, check stock warehouse-wise balance from stock balance report and account balance from general ledger. And the adjust difference amount via journal voucher against warehouse account and cost of goods sold account, assuming stock balance is correct.
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