I did have them misapply a $100k check meant for 2017 (and denoted on check, with SSN and mailed with a voucher indicating the same). Took six months and a whole bunch of the big mean IRS certified mail letters they send you when they mad. This was up to the point of them threatening assets, garnishing pay, intervening in government contracts, etc. Latest comm was great as on the same day I got a letter saying thanks for my payment and all was in order (in fact account for 2017 was now overpaid - would I like that applied to 2018?) and the other was the "this is your last chance buddy".
I would not be surprised that even if they noted it in the system that you called, penalties and interest will be assessed from time they receive check and the postmark date on the replacement check. And without evidence you mailed on 04/02, they do NOT have to waive those penalties and interest.
IRS don't play games.