I am supposing the orginal media (MP4's) will change due to color correction.
NO, PR is a non-destructive editor and source material is never touched. Any changes are contained in the .XML file.
I think he meant that the original MP4 files will come back as something else out of Color with the CC baked in. He will then need to replace the MP4s in the PP project with the newly CC'd files.
Yes, will the "cc'd" files still be MP4's so I can relink and maintain my edits
You can't export mp4's out of Apple Color, so she might have to go with ProRes. The colorist would export an XML to a new sequence that would contain individual clips that (hopefully) match your edits. You need to make sure the colorist (who should be the one to answer your questions) to add handles so you can make changes afterwards.
Hope that helps