I found a huge error in my master's thesis which I defended a year ago I defended my Master's thesis last year and continued on to pursue PhD in the same university under a different adviser. My Master's thesis adviser and I were getting ready to present a paper pertaining to the MS thesis at a conference in two weeks. The paper is already accepted.

Earlier this week, in preparation of showing reports at the conference, I started re-running my Master's thesis code to obtain fresh reports. The results gave me the nastiest shock of my life. The new results I was getting were a magnitude off from the results I had before. I could not believe the new results. Thinking that I had done something wrong in the current run, I re-ran my previous projects which I had used to obtain the results for the thesis document and defense. Even these runs gave me the same results as the new results I was getting. When I dug into it further I realized that I had misinterpreted the value of a single variable which changed all my result values by a magnitude. This reverses half of the conclusions I made and slightly alters the rest. I immediately emailed my adviser for a meeting to discuss this issue. I am meeting with her next week.

In the meantime I am panicking that my adviser or the school board might think that I deliberately presented the wrong values since I was getting better results. I am scared that they might not see my mistake as a mistake or even if they do see it as a mistake, they might take some strict action like revoking my MS degree or suspending me from school or even expulsion. I am panicking. Please advise. Thank you.
Correct the mistake for any peer-reviewed publications (journal, conference, etc). Don't worry about the thesis published at your institution. 

Reason being, your committee signed off in the work as a whole as fulfilling the merits of the degree. Yes, it's unfortunate, but theses often aren't indexed by journal searches, and even when they are, they are generally interpreted with less weight. 

On the bright side, you recognized an error others might not have. Apply this lesson moving forward. In any other case, you'd have to retract. 

PS - I did the same thing during my masters thesis. Didn't sleep for a week.