I would fully expect that this would not be an issue so long as when you do your backing up you've pointed to the top level directory of your
D: drive from Windows and your mounted directory
/media/DATA from Linux. I use DropBox to do something very similar and this service is aware that the same directories from the 2 different OSes are in fact the same and does not attempt to update it in any kind of duplicating way.
If you truly want to know if it's going to be an issue I would devise a small test to confirm, but I would be quite surprised if it did not work identically to how DropBox does with respect to syncing only one time from either OS's location.
From their FAQ
I did find this item in the FAQ.
Question: (justgregit84) This is more a feature request than anything else, but I would really appreciate if there was a way you could bundle CrashPlan for users who dualboot. I run OSX and Windows8 on the same computer, and really wished there were a better way to backup both drives, even though its the same computer. I am going to admit I maybe circumvent the system a little bit by running it on OSX and having that also backup the backups of my Windows drive, but would enjoy if there was a way to consider a dual booting computer as a single computer in subscription terms.
I realize this is probably technically not feasible, but I imagine I am one of many people who dual boots and would enjoy this ability. Regardless, I absolutely love the product, and think its still a terrific value. Thanks!
Matthew Dornquast: Hey thanks! My recommendation is to install it twice on each "OS." Buy our Family Plan or use our free product on the volume you use less.