I want to merge my project with my teams project but missing migrated files

Like the title says, i want to merge my project with my teams project but missing when i do so, not all files migrate.

ex: I migrate my level designers project to mine, his level misses a lot of materials but i cant migrate his whole project because he uses the same folders and it will ask me to ignore or replace the folders instead of merging them.

I am apart of SkillsUSA and I need to merge the project before deadline (June 3rd).

What is the best solution for this?