Interesting... I just tried an experiment. Before doing a Sync from the PC to the Kobo I saved a copy of the database from the Kobo to my PC.
Then I did the Sync but did not disconnect the Kobo, and then grabbed another copy of the database.
Using a free tool SQLite Compare http://www.sqlitecompare.com/
I compared the two databases.
It would appear the Kobo Desktop client DELETED the data for the majority of ePub format books that had been added via ADE.
Then I did the disconnect, and let the Kobo go through a roughly 15 minute process of updates, and again reconnected the Kobo and copied the database.
The entries that were dropped were now re-added.
The only tables changed during this process were:
I think tomorrow I will reset the device and experiment further (as long as I can steal it away from the wife's fingers).