I don't know of any easy way to delete all controllers in any version
of Cakewalk in one fell swoop. I have several "cleaner" programs that
will remove anything not in the whitelist. I also have a program that
specifically removes all MIDI controllers. These programs operate in
batch mode so any file in the working folder will have the changes made,
no need to open files.

I know I have some MIDI cleaners on my web site on the download page
but most likely you would need a different one from what is there. See

http://www.spencerserolls.com/Files4Download.html 

I can also rewrite the program with a different whitelist. All this
code is written so it is not a big deal to modify. I think the cleaner
on-line leaves notes text and controllers so you would need something
different but I either have it already or can easily make it to your
specifications. If you like programming in Perl I can also send the
source for you to play with :)

Spencer Chase
Garberville, California