Is CTM compatible with JUNCTIONS?

I made many junctions such as one that from “C:\program files” to “D:\program files”.
I found that after I’d made some changes in C:\program files and then used system restore, windows would delete my junction and copy all files and folders from D:\program file to C:\program files, which corrupted my folders structure.

Will CTM keep my folders structure?
How do you deal with junctions?
What if I ask CTM to monitor C drive where a junction from “C:\program files” to “D:\program files” exits, but not monitor D drive?

CTM is compatible with JUNCTION feature of NTFS.

For example, if the directory “D:\Temp” specified “C:\WINDOWS\Temp” as its target, then an application accessing “D:\Temp\MessengerCache” would in reality be accessing “C:\WINDOWS\Temp\MessengerCache”.