I just encountered the same thing, as far as I have noticed this is the first time it has happened:
I deleted two books of a series from the device,
Plugged device in, sent (modified) books from Calibre to device, ejected device,
Plugged device in, ejected device,
Only the second book shows series info,
Plugged the device back in, ejected device,
Now both books show correct series info.
This is Calibre 0.9.20 (with Kobo touch beta driver) on Linux, Kobo Glo.