Adding photos from Mac to iPod Touch caused loss of all apps

This post is merely about a somewhat unpleasant experience I had and doesn't pretend to offer any solutions.
I've been using my new 3G iPod for just over a month and had already installed about 80 apps (nearly all free, BTW), 20 full-length movies, several hundred songs, about 100 books (in Stanza) and had set up my RSS reader with about 25 blog feeds.
So, as I have many family photos on my Mac, I decided to add a few (quite a few, actually) to the iPod which is of course very easy to do through iTunes.
However, just after they were added, iTunes started to sync the iPod and, amazingly, it uninstalled almost all of my apps (just a handful were left including those originally on the home page, a few that I had made myself and LastFM for which I had to hack the install as I'm not in any of the three countries in which mobile LastFM is supported.
Getting them back was easy as they're all included in my iTunes.
However, they came back as clean installs which means I lost all of my personal stuff. This included my RSS reader blogs and, worst of all, all of the books that I had painstakingly retrieved by massive trawling of the Internet and then conversion to the epub format required by Stanza.
Nothing for it but to find, convert and reinstall all of them again.
However, now I found that the free Epub2Go app that I had used very successfully the last time around (about 3-4 weeks ago) jus wouldn't work now. Every single PDF file that I tried to convert created an "invalid" message.
Not only that but the other free conversion app (2EPUB) that I'd used the last time around also gave problems. Although the conversion seemed to go fine, the recommended method for transferring the epub files to Stanza on the iPod (using box.net) proved troublesome. What happened was that the epubs uploaded extremely fast (as if the files were tiny). Then in Stanza, the attempted downloads all errored out.
Luckily, however, I discovered Calibre which I've now used for over 100 books and I am extremely impressed. This free app is just streets ahead of what I'd used before which now seem just like silly little imitations of Calibre.
Even in the good times, both 2EPUB and Epub2Go refused to convert some PDF files but Calibre has never shown any similar problem.
And it does so much more and does it more professionally.
Strangely though, my iPod doesn't seem to be recognized as a device by Calibre which means I am unable to directly send my added and converted books to the iPod.
So I use Gmail from Calibre which again always works other than when the book size exceeds the 25MB Gmail attachment limit.