I don’t think they would have any way to know what you paid, would they? As far as I know it would be based on the value of the tickets.
Paging
@Rob562 for comment.
I think they do. When we upgraded UT-purchased tickets years ago at WDW, the CM had to first "price bridge" them, meaning she virtually converted their purchase value (which she could tell simply by scanning them) to the present gate price in the computer system, before upgrading them, so we could keep the benefit of the initial discount price. Somehow, the system "knows" which tickets (which all have an assigned, unique number, like a serial number) were sold directly to guests at full price, and which ones were not.
Rumors seem to conflict about whether price-bridging is still done, and it may depend on whether the CM you're working with knows how to do it properly and is willing to undertake that extra step. Do ask them specifically to "price-bridge" your tickets before upgrading them, and if they don't appear to understand the term, get someone else who does.
There may be another option too: if you haven't used or linked your tickets to MDE yet, UT will let you return and exchange them for the upgraded tickets you want, at their discounted price. At least, that was their policy a few years ago. However, if you already linked them to MDE, that remedy is no longer available.