Unfortunately oxide, you should expect to lose all your settings and apps when you reinstall the firmware as this nokia phone doesn't yet support data preservation. However, you can back up the phone contents using nokia pc suite (which I strongly recommend!). Make sure you've removed any apps installed on your memory card first too. I took my memory card out for the process just to be safe aswell. I then restored factory settings on the phone to eliminate any potential issues there.
Go
here for a guide. (Mods please edit if this contravenes the rules of the forum.)
When I'd flashed I changed the code back too. I didn't lose my 3 access point settings somehow, no, but lost all my apps in the phone memory (though they're backed up of course, and can redownload quite easily). Live messenger can't be downloaded directly, and I lost the 3 quicklinks etc too, but no great loss. Planet3 still works fine if you navigate to it in the browser, and the skype download is unaffected.
The apps you listed, as long as you have them backed up, should be able to be restored afterwards, but they will probably not be retained through the flashing process. The only thing I restored from PC suite back to the phone was contacts. Restoring settings should not be attempted as it can cause big problems when the firmware is so different.
I've noticed a massive improvement in phone responsiveness, and a few new features, plus the camera has improved too, and the GPS is working miles better for me now.
It's fine, and a good process to go through to get the most from the handset, but don't do it if the instructions on that site are too advanced for you (shouldn't be!). Just please PLEASE backup everything first, including themes, sounds, everything!
Hope that helps mate.