If there are any courses in a previous school year that do not have a final grade and a completion date (in the Course Setup screen), the courses are considered "incomplete" and you will get a warning about this when you change to a new school year date in Basic Setup. This is a warning only and you can safely proceed with the new year without any problems. If you want to get rid of the warning, you need to make sure all past courses have completion dates and final grades (even if the final grade is "Inc" - for "incomplete").
Sometimes you may have a course you set up and forgot about - so you don't see it - you think you've completed all courses but the warning still shows up. Here's how to quickly see if you have any incomplete course "hiding" somewhere. You need to do this for EACH student… Go into course setup and in the yellow "Student Level" picklist, select the blank entry (just above the K) that shows up at the top of the list when you open the picklist. This causes ALL courses to show up for all student levels (for this student). You will need to scroll down to see them all, and you can also print this "show all" list if you want.