2000 Taurus Wheel Well
 

I had a blowout that damaged the wheel well liner and when I was going to remove the liner I noticed a clear (empty)reservoir with small tubes on it. One is going into the engine compartment and the other looks like its going forward towards the headlights.

Can anyone tell me what this reservoir is and will it hurt to remove the wheel well liner completely?

If the wheel position is the passenger side front, It sounds like the reservoir could be the coolant recovery bottle. Usually the bottle is made of an opaque type white plastic not clear. If it is the coolant recovery bottle it should have some coolant in it normally. The purpose of the liner is to keep the dirt and flying objects from getting into places where they can do some damage. They are there for a reason and it would be best it it was replaced.