CAn be a problem when some programs do not allow you to install to other than C drive.
Also all programs will have registry entries in the C: drive.
a repair shouldn't be a problem but a reinstall ill also mean reinstall all programs with regirty entries.
The best way is to have a C: drive of approx 20G and use Acronis to copy the whole partition, and back up regularly.
In the event of faiure of the opsystem you can restore the copy in approx 10 mins and be running from your latest backup.