What is the extension on the filename that you are sending? Have you tried copying a .epub format ebook to your Kobo without involving calibre? Does the import screen show up after safely ejecting? Where are you copying the books to on your Kobo? I'd suggest a directory in the root of the exposed storage (I use eBooks as the directory name with the following template in the KoboTouch driver's Save template:
Code:
eBooks/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}
And I am totally uncertain about what you mean by "It shows in the Kobo's own database but it isn't on the Kobo itself"? When you look at My Books with the filter set to All, the books are not visible though the database shows them as present?
You have checked your settings in the KoboTouch driver since the KTE driver is blacklisted in calibre 8?
When you run KoboUtilities Check the Device database, does it return OK?
Have you restarted your Kobo to ensure the in memory and on disk databases are consistent?