I have a Warn winch with a short armature. Is it a big deal if I fit a new motor with a long armaturelength?
Obviously they used the small one for a reason when they made it new

Surely the armature length dictates the length of the motor. So the replacement you are looking at may not fit?

Nope the motor housings are the same length but the armature is a diffrent lenght inside

Interesting!
How much difference is there in the length? Is it minimal? You'd think the armature stack length would match the stator length and so they would not be compatible, unless the length difference is somewhere else. eg commutator bar or on the armature shaft somewhere. But then you'd expect the bearing positions on the shaft to be different.
I've just read your question again, I thought you were refurbishing the motor! sorry!
If you are buying a replacement Warn motor for that winch then I would expect it to be ok. Are there two options still available, long and short armature? Are the stats available for both, power etc? Maybe they've just changed the spec of the wire or something, which has changed the number of coils they can fit in and so had to alter dimensions slightly to get the same field interference.