I imagine your situation is something like the attached sketch (though hopefully not as bad!)
Yes, any downward load on the r.h. span will cause the l.h. span to try to rise up, if that part is not heavily weighted down.
As the hole is about 1/3 the span out from the column, the increase in deflection on that side would not be 10% (as it would be if the hole was mid-span), but probably more like 5% or even less, which would hardly be noticeable. However, the l.h. end of the beam will rise up more than the r.h. side deflects, simply because of its extra length.
One way to prevent this upward movement would be to try to firmly wedge the beam into the notch, but is that possible?