<p>I had a similar situation when I was applying to UChicago. </p>
<p>With three high schools in two countries (with two types of curriculums (IB and AP-style)) my transcript was a crazy mess. This terrified me all throughout high school, so I made sure to keep in touch with all of my counsellors and keep copies of my transcripts and teacher recs. When the time came for my senior-year school to compile my transcripts, I sent emails to my other two schools asking for signed and stamped copies of all my necessary documents. </p>
<p>If you haven’t already, I would attempt to do this. Having two years missing will (most likely) be a problem. :(</p>
<p>About your counsellor recommendation, I agree – mentioning only your academic standing is unfair – when compared to kids who have gone to just one high school. There are hundreds of applicants out there with backgrounds like yours and mine that are considered 100% by admissions staff. My counsellor once told me that sometimes colleges have special committees for 2/3/4 high school applicants.</p>
<p>Want some security? Touch on these things in an “Additional Information” document attached to your Common App.</p>