Do you have students that keep showing up looking like this? Or not showing up at all?

Double check with the student's home district, they may not have the student marked in the district's in-house SIS (Student Information System - Teacher Ease, Skyward, Power School, etc.) correctly. 

If a district does an auto upload/sync, and the student in their system isn't marked to have an IEP, it will uncheck the IEP program in Embrace, every time it does an upload.