Today's findings: the ebook sync is done through
https://mobile.kobobooks.com
It is set in the Kobo eReader.conf
But it is rewritten by nickel on a sync to the original link, so this is currently a hard task to solve.
Another things I found, that the device sends the Collections created on it to the Kobo server, and Kobo keeps this info, if a change is made, then it is sent to the server on the next sync. The eReader can create the missing collections with the sync, if the removal was accidental (a database crash/recovery with old data). Normal removal of collections are also sent to the server. This could be useful - if I can break through the mobile.kobobooks.com