Case 1: CC uses android's Storage Access Framework (SAF) to write the SD card because this is what Android > Kitkat requires. The SAF requires that an app (CC) ask for a long-lasting "permission" to read or write a folder. Unfortunately, from time to time Android forgets about these permissions, meaning CC can no longer write the folder. The usual causes are OS upgrades and device resets, but I am sure that there are random cases where is just happens.
The usual fix is to use CC's Settings / Formats and folders to set the book folder, either the default or the folder for a particular extension, to its current setting. Once you navigate to the same folder and select it, CC will ask Android for new long-term permissions. Note that CC will detect that the source and destination folders are the same and will not attempt to move the books, so this is a relatively fast operation.
Case 2: There are too many files in a single folder on the SD card. The number of files in an SD card is limited. The limit calculation is rather complex, based on the number of files and the length of the file names. With very long file names the limit can be hit at two or three thousand files, perhaps earlier. It is easily hit once one goes by 7,000 files. The fix is the same as the performance fix described in the FAQ [Android] I have added a lot of books and now adding books takes forever. What do I do?