Currently when CCleaner cleans a file that is in the custom files litst, if the file doesn't appear anymore in the system, then CCleaner remove the file item from the custom files list.
Just imagine that I want to delete a file that it's created for a program, only when you run it, and you don't use it every day, the first time CCleaner does the job, the second time it detetcs that the file doesn't exists anymore, but someday you run the program and it creates the file again, then you need to add the file to the custom files list again.
That's my suggestion.
Greets.