If you change the time signature of a section, JJazzLab will use an adapted rhythm for the impacted song parts. This is simply the same rhythm but shortened or repeated to fit the new measure size.
You’ll notice that the adapted rhythm does not need additional channels in the mix console: it uses the Midi channels of its source rhythm (fastbossa.s629.prs in the example above).
If you don’t want the adapted rhythm, juste replace it using the rhythm selection dialog.