That is your problem. You can't mix'n match calibre drivers in the same "target" (i.e., on device) root library (if you hope to keep a consistent on-device calibre metadata state, that is. if you just want to shove books somewhere, that's fine
).
Which means that, unless everything is setup in a specific, per-driver directory tree, you can't mix'n match calibre Wireless with Send to Device via the Kobo Driver (and, to a lesser extent, care has to be taken when using the Kobo driver over USB from both KOReader's USBMS tool and Nickel, as the Kobo driver relies on Nickel's DB, and uses it as a source of truth, while we never touch it at all; I've written about this in the past here). The calibre Wireless plugin should have shouted very sternly at you if you tried to setup a library inbox in a folder already handled by a different calibre driver.
Everything needs to live in its own island (which is why you effectively see different "on device" status in calibre depending on how you connect), otherwise you utterly mangle the consistency of the on-device calibre metadata cache.