- connected and copied over the databases, safely ejected and restarted your Kobo. This needs to be the first step so you have a good database for calibre to work with.
- copied books A, B, C, D & E to your Kobo
- safely ejected and let the books be imported
- Reconnect your Kobo to calibre
- Select all the books shown as being on your device in calibre
- In the Kobo Utilities menu, select update metadata and click on OK.
- In the Kobo Utilities menu, select Store/restore current bookmark. Make sure the Restore radio button is selected and click on OK.
- Safely eject your ereader
As for the bookmark restore, did you configure the needed custom columns and Kobo Utilities is configured to use them so you have some data to restore? See 1st attached image. the 4th image is what the columns look like in my calibre library view.