If after this sync, my employees were placed in a higher level, what happens to the courses they hadn't studied yet?

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

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