Well, re-installing windows is not going to delete the data in your ubuntu install, but it is going to undo the configuration in windows, including the boot loader.
You could try various backups or copying "D:\ubuntu\disks\root.disk" (or whatever), but as you are starting with a fresh install of Windows, why not go ahead and do a traditional installation of Ubuntu as well ?
How to convert Wubi install into regular install?
You can decide what is easier (migration vs. fresh install), but, I highly suggest you back up your data first in case it goes wrong.
