No, the service is colour-blind and will not be worried about which pair you select for it to use.
Personally I would use the blue pair because that would agree with the colours of the pair normally used within a CW1308 specification cable.
Silly question time but what do you expect to gain by rewiring the telephony extension with Cat5e cable? It is a total waste of the cable.
If that circuit does require a re-wire, just obtain a suitable length of either one or two pair CW1308 cable. It has a smaller overall diameter than Cat5e and will be a lot easier to run . . .