An interesting idea. And it triggered some other thoughts. I'll number the ideas for reference.
1) As you suggested, set the sync date on the next connection.
The sync date could be used for that and I have played with it to prove that what you suggest will work. I don't like the need to do it on the next connect. But, I suppose that is simply, disconnect, but I already reconnect to do the series info. The timestamps will all be in a small range, so that makes them easy to find and adjust. Maybe instead of changing by a day, adjust to be a few seconds before the fifth most recently read and still open book.
2) An alternative is playing with the last read dates. When sending books, these could be set to a few minutes in the future for the five most recently read books. That way, when the disconnect and processing occurs, their timestamps will still be later than the new books. Again, I have tested that this works. But, there a problem with this.
Say I set the five books on the home screen to 60 minutes in the future. Then I disconnect and let the processing happen. The books on the home screen will be unchanged. If I open the first book, read for ten minutes and return the home screen, the book I was reading will be in the last place on the home screen.
So, exactly how far ahead is a problem. Five minutes will probably be enough in most cases, but I don't always disconnect immediately after putting books on the device. I think it has to be at least 10 minutes.
3) Actually, if I limit this to just the first book on the home page, this would work very well. And doesn't matter how far in the future the timestamp is set.
4) Of course, there is a more complicated version that settles an argument I have had about how the home screen is populated. Adjust the timestamps but only for books that have been opened "recently". With this, for people who swap between books regularly, these books will stay on the home screen. But for people who only read a book at a time, the ones they opened decided not to read yet, will be replaced by newly opened books. Of course, defining "recently" will be the problem.
What does you think?