You are dealing with two problems.
Sonys rescan the book if the book's file date is not the same as the date in its database. Calibre tries to write the correct date into the database, but sometimes it can't because of timezones. The reader will adjust the date to the GMT from the timezone it thinks it is in. There is no way for calibre to find the device's timezone, so it guesses by comparing the timestamps of existing books to the values in the database. If you empty your reader and send books, then there is nothing to compare to. In your case, calibre probably picked the wrong offset, resulting the dates being wrong from the reader's point of view and therefore all the information in the sony DB being replaced with information from the books. In the future, it would be better to send one book, disconnect & reconnect, then send the rest. This gives calibre a chance to find the device's timezone information. However, there is no guarantee, as there seems to be some conditions where the sony will regenerate the information even if the date is correct.
The covers problem is one that Jackie_w (who has a 650) and I (who doesn't) have spent hours fighting. We have tried to determine exactly how the Sony determines that it needs to rescan the book to regenerate the cover. We haven't succeeded.
Note that both problems go away if you set metadata management to automatic (preferences -> send to device -> metadata management). In this case, calibre will refresh the Sony DB on every connect, fixing the information that the reader unfixed. Note: in automatic mode, calibre will delete any collection that calibre didn't create, so do not set this option if you use other software such as Sony Reader or ADE to manage your device.
It is worth noting that people who never use ADE or Sony Reader seem not to have the regeneration-of-metadata problem. This is entirely anecdotal, and could be nonsense. We *do* know that Sony Reader messes with timezones and date/time, something that has caused grief for this programmer.