What is the version of your Android operating system? Has your Android operating system been updated to 4.4 (KitKat) recently?
On Android OS 4.4 (KitKat) only, Reader cannot make changes to the files or delete the files on an external SD card due to the write permission changes introduced to KitKat by Google. We are trying to provide a workaround for the limitation/restriction in a future release of Adobe Reader for Android.
In the meantime, please try using a file manager/browser to delete the files on your external SD card.
Please let us know if your Android version is not KitKat or your PDF files are not stored on your external SD card.