If after this sync, I was placed in a higher level, what happens to the courses I hadn't studied yet?

Since you will now be at the level that truly matches your skills, you won't need to study the courses from lower levels that you had pending before this transition. 

For example: if you were in Beginner 1 and have been placed in Elementary 1, you won't have to complete the Beginner 1 and Beginner 2 courses. Although you can still study them if you want, these courses will not appear in your progress percentage, but will rather be listed under the "Credit granted" category, indicating that you don't need to study them to keep advancing.