Retirement tax questions

I have the same situation: in 2021 I requested that IRAs held at 3 different institutions - I'll call them X, Y, and Z - be sent as to a new custodian. I called X, Y and Z for instructions on how to proceed with trustee-to-trustee transfers so I wouldn't run afoul of the 1 rollover per 12 months limit.

 

The forms available from X and Y both had mention of the 1 rollover limit so I was very leery, but agents at both assured me that having the checks sent directly to the new custodian would keep me out of trouble. I submitted the requests; checks were sent to and deposited by the new custodian into the IRA I have there.

 

Institution Z said they could only do the indirect rollover. Since X and Y did trustee-to-trustee transfers - or so I believed - and I hadn't done any other rollovers recently, I proceeded, thinking all was well, happy that all my accounts were finally consolidated with a single trustee.

 

My bliss was shattered when I received 1099-Rs from X and Y; since these were supposed to be non-reportable trustee-to-trustee transfers, I didn't expect them. After several conversations with both X and Y -   

- X agreed that I was correct: it WAS a non-reportable event, and they eventually issued a 1099-R that was zeroed out (no entries for amounts and codes).

- Y said no, it was a rollover since they had no way of knowing the receiving custodian actually deposited it into a qualified account. They did say the 5498 would not show this amount on Line 2 if the receiver deemed it a trustee-to-trustee transfer.

 

As expected, I received a 1099-R from Z.  It was confusing due to a separate disbursement made during 2021 but workable.

 

I was leaving on a long trip in early April so I stupidly filed my return using the information from the 1099-Rs that I'd received. In retrospect I should have filed an extension and gotten EXPERT help on filing when I returned but too late now.

 

I got a refund within 2 weeks but have been worried that in time the IRS will come after me about exceeding the rollover limitation, especially since when I finally got the 5498 it had the amounts from all 3 transactions on Line 2. The new custodian didn't seem interested in changing the 5498 to reflect only the rollover from Z, which is what I expected it would be.  They and  2 different tax advisors who I had look at my return  said if the IRS did question it I should be able to prove I was not in violation, but I don't want to wait and worry for 3 years to find out they're wrong and and owe a pile of penalties and interest. 

 

Do you think I'm in trouble with this?  I am trying to engage an expert, IRS Enrolled Agent advisor but they're all on limited staffing right now.