I had this problem too.
I solved it by using MixMaster.
In MM you can load 2 midifiles.
Load the midifile with the chords
and the midifile that was changed in Cakewalk.
Copy the chords from the midifile with chords
to the midifile without chords.
Pay attention to do this at the same MBT
as the midifile with chords.
Wrong way to
Download Cakewalk free by bandlab it save the chords
When you work for long time with Cakewalk use the new version
Don't need to go to another Prg.
You have to copy nothing the chords are already in the recorded keyboard midi file
by load it in cakewalk
I use XgWorks
Even a better prg
It got a chord track
It load the midi file the chords are on the chord track
Or you can make a chordtrack with the mouse
You can remove the arranger tracks in your midi file
Take a style in the prg.
Set it as parts under the chords
You can use the intro endings breaks and variations
Expand to midi
You can also change a style on any point in the chordtrack
Or use a double style layered the one on the other
You can also make differentt time signatures like 4-4 3-4 2-2 in the chord track