Clean up and consolidated Logic X but getting "missing files" that are not in the session

Hello,

This is what I did for your exact problem that I was having:

Open Logic and open the project in question. Say "skip" to the nonexistent files. Then click Window - Open Project Audio (cmd-8). In this list is all the files associated with your project. As you scroll, you will see files that have a "!". For each file with a "!", click it then hit the delete key. That will delete the reference to the file for the project. Do this for each "!" file. Make doubly sure that you are only deleting the files with "!". If you select an actual file and hit delete it will delete it without confirmation.

I did this for each "missing" file and once I saved the project, the "missing audio file" message never appeared again.

Good luck! Just remember that this file deletion is non-confirming and you must be careful when selecting files.