Are you trying to replace the lost material? Or just fill holes and structurally it's ok with the holes in it? That may significantly change some people's answers.
A bit more background on why always helps tailor the answers.
I have 3 LVL 1 3/4" x 11 7/8" x12' a 5/8" attached together, a hole was drilled from the top of the center LVL to the bottom for a hold down treaded bar, which was in the wrong place. This is about 12" from the wall that supports the beam. Can I fill in the hole with an epoxy, if so what type?
Similar to jayrod12's comment, I wouldn't bother with filling the hole with epoxy because I would not consider that an effective structural repair for shear or flexure.
I would consider:
1) Checking to ensure that the two outer plies can handle the shear on their own.
2) Adding some concentrated fastening in front of the hole to transfer the shear of the disrupted ply over to its neighbors.
