stay vacated automatically due to Apex court order

Redraft facts vis-a-vis your query, which is vague.

The Hon’ble Supreme Court also emphasised on the accountability of the courts while granting stay of proceedings and held that such matters should be disposed of in two-three months without allowing any adjournments. To ensure a speedy disposal of such cases, the Supreme Court directed that a stay of trial proceedings before civil and criminal appellate/revisional courts ordered by a High Court or a court below High Court shall automatically expire in six months, unless extended by a speaking order. This direction has been reiterated by the Hon’ble Supreme Court on October 15, 2020 in MA No. 1577 of 2020 in Criminal Appeal Nos. 1375-1376 of 2013.

what will be the effect of pending case in hc under sec 482

You have not posted the material facts.