Possibly need to delete and re create a partition. Need Advice.

We have an SBS 2003 server with 2 partitions. The OS is on C: and all of our files.shares are on E:

We are using a backup device from Datto (http://www.dattobackup.com)

Back ups on E: are not able to be restored. Basically the way it is supposed to work is  you mount the recovery point through the Datto box and simply browse and restore the files.

This works fine with C:

After weeks of the engineers at Datto working on this I have been told

"After further investigation, we have come to the conclusion that the partition table for this volume is corrupt and un readable or recoverable with our systems. If you would like to continue using our device, the best course of action to do would be to copy all of the data off of the partition, reformat it as a primary partition using NTFS and reload all data back onto it. Before doing this however, it would be best to stop the snaptovm agent. We believe this will resolve your issue going forward. I apologize for any inconvenience this may cause."

I guess my question is, does this sound correct. Also what are we talking about difficulty wise? I suppose it wouldn't be to tough for me to pull all the files on E: to an external however I am worried about something going wrong when deleting that partition and recreating it.

Any help is very much appreciated.

Thanks