I found myself in the situation of helping a friend reinstall windows on a system which also has Ubuntu on it. In other words, it was a dual boot system, and we were both afraid that re-installing Windows will overwrite the Master Boot Record (MBR) and make it impossible to boot into Ubuntu in the short term. So we devised a plan, with a little help from google to backup his MBR before reinstalling windows, and then restoring it after reinstalling windows.
Create a backup of your MBR by doing a:
$dd if=/dev/hdx of=MBR-backup bs=512 count=1
That should read “create a disk dump of the input file, which is /dev/hdx (change to hda, or hdb or sda, depending on where the MBR is on your computer), and save it in the output-file MBR-backup in the directory from where the command is issued. Backup the first sector only, while you are at it”.
Now that is the backup of your MBR. Restore it later using:
$dd if=MBR-backup of=/dev/hdx bs=512 count=1
Again, change hdx to hda, or hdb or wherever the MBR needs to be restored to. You may have to use a live cd to restore the backup since you will be unable to login to Linux after you reinstall Windows.
As with all other advice, take this with a pinch of salt, and search on google for a solution to your problem, understand the solution and then embark on your mission!