Just found out that my business returns were never filed in 2022. Anything special I should do when sending them in?

I'll be submitting the California form 100S to the Franchise Tax Board. The return was completed by a pro, but it was my job to print and mail them, I either neglected to or they were lost in transit.

The business overpaid in estimated tax payments, so AFAIK we won't owe any penalties. It will be nice to get the refund check. I'm just wondering, is there anything I should do other than just mail them in as usual? Should I flag the envelope in any way to help ensure that the FTB doesn't mistake them for this year's return (which was already filed, processed and refund check mailed by the FTB)?

Also, I have no way right now to determine if the Feds got our 1120-S that year, either. My wife is the Designated Official of the company so she is eligible to have an IRS business tax account, and we'd set one up online right now, but she has some SNAFU with her ID.me account and it may be until the gov't shutdown is over before she can get it fixed. Is there another way to find out if the IRS received our 1120-S? For instance, is anyone answering phones or supporting online chat at the IRS during the shutdown?

Any helpful advice or guidance greatly appreciated, thank you!