No reply from my thesis adviser
Formulate a version of your thesis without the problematic results. Write it up, at least as an outline, but probably more completely. Analyze it.

But also consider the fact that the results that aren't as expected might invalidate some expectations and lead to a different result. If that is the case, it may be that the "odd" results are pointing you to something important. If so, write that up, instead. Analyze that version. 

Then give either or both versions a good look and see how it appears to you. Do you have any results of significance that will carry you to your degree? The next step is to show this work to your advisor and get whatever feedback you can from them. Point out that you have dropped one aspect or changed the focus, but that it holds together, assuming you judge that to be true. 

Then take whatever advice you get from the advisor. I suspect you will be told it is fine to proceed, but if not, work out a plan for completion with the advisor. 

In general, "not as expected" is a research opportunity, not a setback, but you can probably be successful on one of the two paths.