[dba-Tech] Server harddrive updates

I have had to do updates on one of my servers. 

The server, in question, has 4 x 2TB drives and the time it takes to run a
full check-disk is about 6 hours. In the meantime, I have had to re-direct
to a friends site to maintain all of the web support.

Question: Is there anyway, software package, or method to run in the
background as the system will currently only do a thorough check-disk in
boot mode which means the whole server is effective down until the process
is completed.

TIA

Jim