Brief answers:
1) if you library points to the new music on your external drive, you should be fine. You should be able to do a check to see which files will be deleted and which will be added to your ipod. Plug your ipod in and on the iPod screen in Media Center, click on the "Check Sync" button. Media Center will show "On Device" if it recognises the track on your iPod as matching something in your library, or "In Queue" or "Delete" as other options. You might find that the music will be deleted and re-synced, so it might just take a long time for it to essentially do very little!
As long as you have all the music on your drive, there is relatively little danger in "deleting files not in sync list". As I say, you might delete a whole lot of files, but then copy them straight back... There are a number of factors that dictate what will happen in this scenario!
2) You can manually delete songs on your iPod. This is tedious though...