As a quick example, say you're using Windows 7 64-bit, your user name is Donavin69, your Dropbox folder is located in a "My Dropbox" folder in your user profile folder which is located on your C drive, and you have unique folders in it named KoLmafia1 through KoLmafia3. The stable files are in the KoLmafia folder in your 32-bit Program Files folder.
From command prompt... only going to do KoLmafia1, because it's already getting long:
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\buffs"
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\ccs"
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\data"
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\images"
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\relay"
rd /s /q "C:\Users\Donavin69\My Dropbox\KoLmafia1\scripts"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\buffs" "C:\Program Files (x86)\KoLmafia\buffs"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\ccs" "C:\Program Files (x86)\KoLmafia\ccs"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\data" "C:\Program Files (x86)\KoLmafia\data"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\images" "C:\Program Files (x86)\KoLmafia\images"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\relay" "C:\Program Files (x86)\KoLmafia\relay"
mklink /j "C:\Users\Donavin69\My Dropbox\KoLmafia1\scripts" "C:\Program Files (x86)\KoLmafia\scripts"
This removes your local account's buffs, ccs, data, images, relay, and scripts folders and links them to the local shared editions. The rd /s /q means to nuke the existing folders, because mklink needs a hole to connect to... can't link to a folder location that already exists. Then we create directory junctions to those folder locations.
Note that you WILL want to move/consolidate any files in those folders to the shared locations before you wipe them, since they're not coming back.

Alternatively, you could rename the folders rather than remove them and then you could always move files in later.