Let me give you the professional stress disposition I have given 1000's of times on air transpor( airplanes to maintenance.
- "break sharp edges" and/or blend smooth removing minimum material.*
- No sharp edges (maroon scotchbrite pad on rotary tool works well if you are careful and controlled). Get some scrap and practice, other wise hand work it (SLOWLY) under GOOD LIGHT. and magnification.
- Final Surface finish 63 rms (root mean square) accomplished with fine (light grey) Scotchbrite pad and is as smooth or smoother than original finish,
- Measure depth of material removed and note here: _____________ Max depth is x.xx. if depth is great reconvene with Engineering.
- Prime with (spec) and pain (spec) to match as required. (Note you removed clad so you need to use corrosion protection)
- Demine what caused the issue and correct it before installing spar in center section.
- Reassemble structure
* Minimum material removal means do not make it deeper, wider or longer than needed to remove damage and make smooth. in general 20 to 1 blend ratio for deeper gouges. Say you have a sharp 0.010 gouge (I think yours is much less), you would have 0.4" wide blend, or 0.20" each side of damage as you blend out.
If you are in an area of where fastener sits you may NOT want to blend there, adjust the blend ratio, say 10 to 1. In extrema cases (which your is not) may need to blend around the hole or spot face the land where fastener seats. Do not do this. It is just an example for much larger and deeper damage at edge of hole. This is typical of corrosion repair, which you are no where near. However if damage is across a fastener hole it will be a little more tricky and require more time and careful blending to remove damage and maintain flat landing for fastener.
In general aircraft are designed with rework allowable expressed in percentage of total thickness (example 10%) or actual dimension (0.030"). NOT SAYING THIS IS ALLOWABLE, JUST EXAMPLE for transport category planes with thick metal, not sheet metal. In the case of Air transport planes there is a SRM or Structural Repair Manual with allowable damage. In this cases call Van's.
I'm sure Van's Aircraft will say scrap the spars and buy a new wing kit... Ha ha. Kidding. You are doing the right thing by asking. Eye balling it this will have zero point zero zero effect on the over all strength of the wing. Another way of saying it, this is not the weakest or most critical part of the wing for any flight load. The wing roots are overbuilt intentionally. Van's did not cut the margin of safety to the bare minimum. However we can not allow damage or be cavalier about it. It always has to be addressed. During the manufacture of large jets you might be surprised how many Booboo's there are. They are all documented, addressed and recorded and those records or rejection tags and dispositions go with the plane. Yes in a few cases for big screw ups sections of fuselage or whole wing were scrapped. Rare, but it has happened.
I recommend you find out what is scratching the spar. You may have some issues in your center section to address before plugging them back in.