I don't think there's a simple way to change the time signature of a style file or song file.
The way I'd probably do it would be to split the style into its MIDI portion and non-MIDI portion using the "Style Split and Splice" program--
http://www.jososoft.dk/yamaha/software/sands/index.htm.
Then I would import the MIDI portion into a DAW so I could work on the MIDI tracks using the piano roll editor. When I was done editing the MIDI portion in the DAW, I would export it back to a MIDI file, then use "Style Split and Splice" to rejoin the MIDI portion and non-MIDI portion back into a style file.
The actual editing is where things would be tricky, and it's difficult to give specific advice on how to proceed without knowing specifics about what you want to do. For instance, do you want to actually delete a beat and its associated notes from each bar of music? Or do you want to keep all of the notes more or less intact but shift the bar lines as it were, such that 3 bars of 4/4 music will become 4 bars of 3/4 music?
It should be noted that MIDI files typically contain many types of non-Note events which do not show up directly in the piano roll editor, but are instead displayed as automation lanes. When you're deleting any Note events or moving them around, you'll need to pay attention to those automation lanes as well, to make sure that any non-Note events are also deleted or moved around so they remain properly aligned with the Note events that they apply to.
