You may be asked to check all the drives in your server for errors as a troubleshooting step, or you may be experiencing file conflicts or other errors and need to do this. If you simply open a command prompt and use chkdsk on each drive, you may spend many hours waiting (and rebooting your server to force the dismounting of drives).
You can use the following batch file to force chkdsk on all your drives. Copy the code below and paste it into notepad, then save it (on your server) as e.g. "checkall.cmd":
net stop pdl
net stop whsbackup
chkdsk D: /x /r
chkdsk C: /x /r
for /d %%1 in (C:\fs\*) do start chkdsk /x /r %%1
Log in to your server, copy the file to the administrator's desktop, and run it in a command prompt from there.
When you run this file, you may see a variety of warnings and network health notifications from your server. These are normal, and are a result of forcing the dismount of all storage volumes. When the batch file finishes running, note any errors then reboot your server.
Note: rather than watch like a hawk for errors, let all the chkdsk runs finish unmonitored, then (on your server) check the applicaiton event log, source winlogon, for chkdsk reports.
I'm not on the WHS team, I just post a lot. :)