Today, I bought a CTR low autogun and upgraded it to a needle shot. However, the checkbox to transfer UV appeared late, and it only appeared after i clicked the craft button. It was however, checked.
Oddly enough, after that, I got two new UVs- gremlin low and undead low. According to the wiki, "When performing an upgrade, the knight chooses whether to keep the unique variants (UVs) on the precursor. If he or she keeps the UVs, then the upgraded item will have those UVs, with no chance of more or better UVs. If he or she discards the UVs, then the upgraded item has the same chance of acquiring up to three UVs as an item made from scratch, without a precursor."
So there should have been no chance of me getting more UVs.
It appears that I got to both keep my CTR UV, and yet roll for new UVs as my game was slow to realise I had a UV.
EDIT: I also realised that it is possible that due to the lag, and the fact that i clicked craft before the option to transfer my UV appeared, the game rolled for UVs again, and got CTR low, gremlin low and undead low all by chance(so the recurrence of ctr would be a random event)