I agree with Jerry, though I don't have specific proof. My expectation is that eQSL will properly treat uploaded ADIF files that use the <MODE:5>PSK31 tag and convert them during incoming processing to the PSK/PSK31 mode/submode. It's only the previously-uploaded files that would have the mode wrong and thus have to be converted.
I can confirm that later when I do an upload, since I know for a fact that my ADIF uploads will NOT be using the v3.0.4 format.
One note though: if you have more than one eQSL account, you have to run the utility on EACH account. You can't just run that on your master account. So those of us with multiple accounts due to callsign variations and/or station locations have to run it multiple times.