Duplicate Cakewalk Content Folder

When I upgraded to Platinum from X3 several years ago I decided to follow advice in one of the Garrigus books and put the Cakewalk Content folder on drive E:, separate from the program on C:.  At that time I adjusted many of the the Prefs > Folder Locations accordingly.  I've done two Platinum upgrades via Command Center since then, but only recently discovered that there is a CmdCtr content path and that it is pointing to C:\Cakewalk Content, not E:\Cakewalk Content.  I now see there are a mix of folders in both locations, some of which I've reconciled and copied over from C: to E:, but there are a few (eg, Rapture Pro, Drum Replacer, Anderton) that I'm pretty sure can't just be copied over.  And Sonar itself is looking at C:\Cakewalk Content; I know this because if I rename it and start the program I get a message about missing preferences or some such and it creates another Content folder on C:
 
I want to fix this before doing any more upgrades.  I was going to change the CmdCtr's path to E:\Cakewalk Content, thinking that it would then do an inventory of what was missing from E: and let me reinstall that stuff.  But when I go to make the change I get the message, "Changing your content path may cause bad things to happen.  Would you like to copy these contents and change your path now?"  
 
Now maybe doing this will be OK, but clicking yes to a message like that is not something that gives me a warm and fuzzy.  Has anyone experienced this problem or otherwise dealt with how to recover from duplicate Cakewalk Content folders?  (I had no idea CmdCtr kept the content path--I just stumbled on it by accident.)
 
Thanks in advance for any input or help you can provide.

I would change it and take note to where the new content is going.
the worse thing that's going to happen is you'll have to copy those files back to the C/Cakewalk content folder again.
When you think about it, this folder is not really that large (except for the sample content, The loops that is which can safely be deleted if you don't use them).
I have a 255 SSD HD and I keep all my content on C/ (the Cakewalk content)
Its the large sample library's you should really be worried about (Kontakt, BFD, EZ Drummer, EXC).

Thanks to you both for your input. Decided to live with the two Content folders and went ahead with the update. Altho I'm having some of the same problems other are with the latest release, as expected, nothing major caused by the duped folders. Forced me to get my MIDI content folders organized finally! That was good...