Noting that the IRS has had difficulty promptly adjusting their records to recognize that a Form 5558 has been filed, there should be no problem to solve. Timely filing a Form 5558 to extend the filing deadline for the 5500 and the 8955-SSA is all it takes. IRS approval is not required. If the Form 5558 is completed properly and submitted on time, the IRS has ceded all authority to reject such a filing.
I'm guessing you haven't had the IRS send a letter to some of your clients claiming a Form 5500 was filed late and a penalty will apply because the IRS did not process the 5558 timely. We had one client receive two of those letters in a four year period. After getting a power of attorney signed and wasting time on hold, the matter was quickly resolved once I was able to speak to a live person at the IRS. I don't enjoy extra non-billable work and having clients think we missed a deadline that we did not miss just because the IRS waited until November to process some extensions filed in July after they sent out late filing notices in October.
As I said, there SHOULD not be a problem with this. That doesn't mean there isn't.
If it migrated to EFAST2, who would be able to file a whole batch of 5558s at one time (as in one 5558 for every single ERISA client)? Would plan officials authorized to sign off on the 5500 filing have to get involved? And (as much as I hate to suggest this) what guarantees are there that submitting a 5558 through EFAST2 would keep the IRS from failing to notice that it had been submitted?
How often does the IRS assert that timely filed 1040s were late? Why do they do so with the 5558s, which (one presumes) come to them in much smaller quantities?
I'm cautiously optimistic that electronically filed 5558 would not be worse than the current paper filings. For the possible issues, I see simple solutions.
1. If migrated to EFAST2, who could file a whole batch? I don't see why it wouldn't be possible to batch file 5558 electronically. If the e-5558 can be filed without a signature like the paper 5558, third party software can easily come up with a batch function. Even if you had to extend the plans one by one, it shouldn't take that long for the average service provider...
2. Would plan officials have to get involved? Maybe, but again, not the end of the world. You simply send out authorization for the extension when you collect your annual data.
3. Of course there are no guarantees, but can it really get worse?
J