As part of my Degree, it’s a requirement to give our source code to the uni. However, some of my files contain paid assets. Should I remove the paid assets from the files or put a license text file stating that they should own a license in order to use it?
Yes you should remove paid assets, as their redistribution is forbidden by license agreement. Unless siad assets are originally under open license or you have written permission from their creators.
For your submission, after removing the stuff you cant redistribute, you should probably also document what assets you’ve used, what they were specifically used for, and specifically delineate them from your own work.