Wǒmen duì wán zhàng cái fāxiàn shǎo le yìqiān kuài.
Only after reconciling the accounts did we notice we were short 1,000 yuan.
Tips
grammar
对账 is a separable verb: 对了账 (duì le zhàng, reconciled the books), 对完账 (duì wán zhàng, finished reconciling). Avoid treating it as one inseparable unit.