No Red Avid AMA plugins installed, althought that link you sent me says that plugins are installed if using MC 6.5. Are the plugins required to be able to re-link media?

I am targeting the root R3D folder when I try to re-link.

Just to be clear about where the media is and where it came from: the raw footage was transcoded from a shuttle drive, then the same raw media was copied to a separate drive (drive #2). In Avid, the AAF/MXF files point to the original location of the raw media (the shuttle drive), so I need to point it to drive#2. 

julesnurrish:

Are the plugins required to be able to re-link media?

To the best of my knowledge yes, they are. So definitely download and install the appropriate plugins.

julesnurrish:

In Avid, the AAF/MXF files point to the original location of the raw media (the shuttle drive), so I need to point it to drive#2.

Try selecting all the R3D clips in their bin, then hold down CTRL + SHIFT (CMD + SHIFT if on Mac) go to the clip menu and select "unlink". Then attempt to relink to those clips targetting only drive #2.