Since ondevice does not persist if you restart Calibre, I use the Reading List plugin to keep track of what books are on my device when disconnected.
Instead of 'send to device' shortcut I remap it to send to 'reading list'. Next setup the program to manually/automatically 'Replace device with list, add new items only' (this adds/removes except overwrites because in my case it would remove the 'im_reading' collection the kobo uses).
When disconnected you call up the reading list, add/remove books to sync later. Reading List can also add a tag so you can do fancy stuff like column coloring, etc.
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