If i were to enchant a weapon with 25 points fire damage for 4 seconds, and i attacked an enemy twice in under 4 seconds, would they take 200 fire damage total?

No. However, if you enchanted TWO swords that way, hit with one, switched, and hit with the other, then yes, they'd take the full damage.

I think in the case of a single sword, it just resets the timer.

As mentioned above the timer is reset.

So if you strike, then strike again in two seconds with the same charged weapon then you'd deal a total of 150 points of Fire Damage.