If accuracy, meaning comparison to a standard, is really you're concerned with, then you should be using a special limit-of-error thermcouple. The commercial catalog on my desk shows that extension wire for type J and type T comes in special limit of error, but types K, N & E do not. For a long, 100m run of extension wire, you might consider using a type for which special limit of error extension wire is available. I have no idea of whether the availability of special limit-of-error extension wire is industry wide or just this vendor.
Routing the extension wire to minimize thermal gradients across the extension wire (as opposed to the desired hot-to-cold-junction gradient) will minimize the potential for leg-to-leg errors in those gradient.
And I must ask, why not move the transmitter and achieve a short run to the T/C and do the long run on copper with 4-20 or whatever bus the transmitter talks?