It probably would be ok since you are bolting two flanges together, and in effect reinforcing the flange....
The safest place to drill holes, weld, make changes, etc.., is dead in the center of the web. It isn't doing much of anything but taking up space and adding weight.
This is not to say that the web isn't doing anything important, it is. If it wasn't there, the flanges would be a pair of floppy pieces of steel, incapable of even holding their own weight without drooping. The web keeps the flanges apart, and allows them to act as major tension and compression members, and the flanges keep the top and bottom of the web from buckling, and allow it too to be a major tension and compression member.
Take a 11 inch long 2 inch wide strip of paper, and observe its characteristics. Then bend the top 1/4 and the bottom 1/4 so it is shaped like a frame. Notice how much stiffer it became.
-Chuck