I've got a suggestion: Try exporting all of the .flps except for one (the one you want to stick with as your master, ideally either the first verse/intro or whichever has the most data) to midi files, then import them into the master flp. You'll still have to create the instruments by hand, but you can at least get the sequencer data this way.

Also, you could save all of your instrument settings from each part of the songs into presets and load them into the master.

Let me know if you need more details about how to do any of this, or if this doesn't make sense.

-David