If I understand you correctly, you are saying that if you select the same folder using CC's Settings then it works from then on. If this is correct then I think you are "victim" of the consequences of certain CC manipulations.
When you initially install (Amazon) CC, it sets itself up to access the "Books" folder using the native file system commands. This works on Android 4 up. However, if later you change the default folder to something else and if you are running Android 5 or later then CC uses the (horrible) Android Storage Access Framework to read/write the folders. The permissions that CC gets in that process will often not survive a device change or an OS (Android) upgrade. Thus, if in the past you:
- changed CC's book folder to something
- changes CC's book folder to the default
- upgraded Android or changed devices
then you must use CC's Settings / Formats and folders to reacquire permissions to the folder in question.