the bank with the actual item won the battle for the funds.
The problem here is you didn't go to battle, and you may have missed your chance. This isn't an automatic claim -- you have to realize you have a claim and then join the battle to win your claim. You may have sat this one out too long.
You can try, but a lot of time has passed. Look at Regulation CC section 229.34
, paragraphs 34(f), 34(i) and 34(k).
In May, when you got the return, you should have tried to identify which bank took the check in a mobile deposit. Of course there is nothing on the check you got back to identify that other bank -- you have to contact the paying bank and ask for its help to identify the other bank. You can even ask them for a legible copy of the reverse of the check (they don't have to provide it, but a sympathetic bank might do it). That gives you the info you need to be able to enter an indemnity claim under 34(f) against that other bank.