lt will get rejected if by the IIRS if IRS does not have an accepted S election on file (99.99% of the time. I've heard of a few cases where the issue arose years after filing S corp returns).
ProConnect doesn't know or care if it really is an S Corp.
My client filed the paperwork and then submitted the S-Corp filing. He also did not have a letter as he had moved. On the S-Corp filing, he added comments explaining what was done. Nothing was rejected and he received another letter confirming the election in the mail.