Ok i started a Sand Patch service with the CSX SD40-2 not 5 minutes after that i get a Rare Achievement saying “First Steps in the Dash 2: Drive 5 Miles in the UP SD40-2” i dont own Cane Creek, this tells me the Coding Bond Between the CSX SD40-2 and the UP SD40-2 is closer then it seems
This isn't a one-off. The Class 47 achievements, for example, work on both the WSR one and the NTP one. The SD40 achievement appearing for you is likely as intended by DTG.
Its just weird but it makes sense the CSX and UP SD40-2s are very similar so getting an Achievement for one should count for the Other
DTG try to do the achievements on a 'per-train' basis. If you go into your stats menu and pick by train, the UP and CSX SD40-2s should be together, like the Class 47s and Dostos are. I'd quite like to test this as well with the Peninsula Corridor SD40-2 (which are annoyingly known internally as being in Y3b livery...).
I got some trophies today too, as I was messing about in Sand Patch moving some locos around the yard. Lots of ‘first steps’ taken in the familiar old trains. It took me a moment to figure out what was happening then I remembered getting a trophy for HRR before buying it in TSW2020 because of the reused BR 422 from RRO and I just had a little laugh about it.