For 1040, file a 1040x. Here is a good article https://wealthyaccountant.com/2018/02/21/how-and-when-to-file-a-superseding-tax-return/ There is no X box for superceding, as mentioned in the article, but you can e-file an amended 1120s OR go paper and write SUPERSEDING RETURN across the top of the form

https://accountants-community.intuit.com/questions/1701170-need-help-superceding-a-corporate-return speaks to filing both on paper. 

https://www.irs.gov/businesses/corporations/amended-and-superseding-corporate-returns indicates the box not being on the form, but select in the software. Lacerte does not seem to support this, so it would mean paper filing. 

I WOULD FILE BOTH AS PAPER RETURNS.