When installing new applications, most installers give you the option of the install directory, at that point you should re-direct it to your C:\ root. If you do this AFTER you installed the program in the C:\Program Files directory and copy it to C:\... you're gonna have problems. If you want to change the directory AND have your applictions work, you will have to uninstall the program and reinstall it into your desired location.
As far as data loss when copying files from CD's, make sure you view hidden files, before copying anything. If the CD has any files with the hidden attribute, they will not be copied over if you can't view them.
What does change is the attribute of the files. Any file copied from a CD has a 'Read Only' attribute, if you want to edit any files you will have to remove that attribute.