had exactly the same issues when i first used spectral layers 7 and now i never ever use it anymore due to this exact thing, cant believe its not been fixed yet
the only time i use spectral layers now is standalone.
it would make more sense for the ara audio to be in a subfolder in the same way AUDIO is a subfolder, there should be a “ARA” folder
NOT audio saved in the .cpr file is daft! (apparently its the ARA standard for Portability)