Have you tried? With the device connected
search ondevice:true : <select all> :
<right click the Kobo utilities Plugin icon>Update metadata in device library:
<accept the next screen which will have those needing update marked> (sorry, I do not have a screen capture for this. BTW this is the same place you resend the TOC when you edit a books structure. Kobo store the TOC in its DB during the first 'processing' and not again unless yo force it this way)