[stumped]

the kobo for android app has to import books into its own database, before they can be seen read in the app - other android reader apps, like moon do not behave like that.

so calibre can put book(s) onto the device, but it cannot make the kobo app import them. you have to do that manually by opening the app to scan for books that it can import

also, because the app relies on a self-maintained database, if that gets corrupted you are in all sorts of trouble.

try using a different android reader app and see if the problem goes away.
or if you must use the kobo app, carefully study its help files ( if it has any ).

its been a long time since I used that app, I suspect that kobo have mostly lost interest in supporting it, as they no longer sell android devices.
A Alf has no effect on whether books show up or not. it only becomes relevant if books show up but cannot be opened due to DRM