I use iTunes, not expertly, but anyway here's a few thoughts.
Ultimately all your music is held in Windows folders which you can browse out in Explorer if you like. Have a look in My Documents\My Music\iTunes\iTunes Music.
So your music is still there. What I did very early on was to opt to manually manage everything - the library and the ipod. I can't remember exactly how it's done, but if you go to iTunes Help and search on "manually manage" it will come up with a few entries, one of which is how to manually import into your library and ipod. If you do this, then you have total control over the contents of your library and ipod and don't have them synchronised every time you make changes. This way you can keep independent libraries on different computers, e.g. at home and at work.
Furthermore, you can delete stuff from your iTunes library but opt to keep the files (in Windows) which then you can manually reimport if you decide you want them again.
I hope this helps, but I know I haven't explained it terribly well.