Potential plot hole regarding Zero and Omega???

So I was looking at RevoReploid's video that did a breakdown in regards to how Zero and Omega's look weren't just an art style choice but what they actually looked like during the events of the elf wars up to the Zero series. There's something that's been bugging me in regards to that, if this is true.

If they upgraded and transferred his body from his original body (X series) into a brand new one that Omega would eventually steal, then why would the scientists be studying the new body (the one we see in MMZ3) and separate Zero still? The ORIGINAL body from the X series was the one with all the power from Wily, so if they made a new body for Zero that SOMEHOW had the same properties as the ORIGINAL body from the X series, wouldn't that mean that they already had an understanding of how Zero's body worked in order to create him the new one Omega stole, otherwise why were they studying that body and not the ORIGINAL one from the X series?

I hope this made sense, because I don't get it.