Much of my music uses repetition with overlaid changes. I sometimes want to keep a section repeating as-is but with a different flavor: different filters, EQ, etc.
One approach I’ve found useful is to set up alternate send tracks and use automation to switch among them.
I wrote up a blog post describing this.
http://neurogami.com/blog/neurogami-renoise-automation-and-multiple-send-tracks.html