I have had the experience getting upgraded on one leg at time of OLCI, and aborting the checkin so that I could try later via OLCI for the upgrade on the second leg. I did not lose the one upgrade that OLCI had given me even tough I did not complete the check in process.

Unless you get the upgrade at time of OLCI, I think that you are better off waiting to try again or perhaps allow EUA to run. I just did this and found that EUA upgraded me at some point between my hours apart attempts to score the upgrade via OLCI. Such would not have happened if I had been checked in.