I should think the Ebooks app would be check your SD card upon opening for any PDFs (or any compatible files it can open) so they list for you. (It would probably be the same for a music app which plays MP3s, it will search out any MP3s available so they list.)
So deleting any files will delete from any app that lists them. You could try saving your files instead to the internal memory Mobilesheets can use, then see if Ebooks lists them. (If you try this, make sure you back up your MS files first before you transfer them.)
So deleting any files will delete from any app that lists them. You could try saving your files instead to the internal memory Mobilesheets can use, then see if Ebooks lists them. (If you try this, make sure you back up your MS files first before you transfer them.)