Just an update. So I figured out a work around. I transfer my books to iTunes - by dragging and dropping from Calibre into the Kindle app sharing folder. Then I open DiskAid and move them from the general folder to the ebook folder.
When I just did the first part (dragging to kindle/iTunes) the books wouldn't sync across my iPad and Kindle. By doing the second part (moving to the ebook folder) they sync perfectly. These are for sideloaded non-amazon books.
I still wish there was a way to copy directly to that ebook folder. But this works
