it kind of depends on the workflow you are used to. I mean, personally i would just throw it in recylce or edit it out with audicity back and forth. If the Beats per minute is the exact same you are using inside the song that you are trying to create, then Dr Rex will probably be your friend in this setup.
Cut the parts that are troublesum and slice them independently. The trick in most some cases is that you are able to fake the tempo changes with using a bit of delay, reverbs and pitch modulation (which can also become a bit weird as an outcome, but its a bit trial on error).
A sliced rex file can be loaded up inside the NN-XT and allows lot more control for pitch correction on that matter (using the Modulate Envelope of the remote programmer of the NN-XT).
It is probably all a bit trial on error I guess since you also mentioned 'touching in the dark' with this. I can only guide you in the process on my own experience.
