Something like this:
Join every x blocks (with x being the number of blocks), in song/selection, maybe with a block offset.
Split song/selected blocks x times.
To do this manually would take quite a long time, especially in long songs.
What is a block?
That’s a pattern. Maybe the pattern split+ tool will help you. http://tools.renoise.com/tools/pattern-split-plus
Joining is fairly fast and simple using the native join feature. You’ll find it in the right click menu where your arrow is pointing.
Your right I was going off make block unique. 
I know joining is simple but it would need doing quite a few times in a long song. I already have the split tool which is good for single patterns but not all patterns at once.
The reasons for this are mainly for automation, DBlues Automation From Notes for example you have to repeat the generate for every pattern which can take a long time for a minor change, if you could join every pattern, run the script, then split back, it could be done in a few clicks. It would also make longer curve automations a lot easier.
I just thought about this and it would need to remember the state of the mute on/offs and other things like blank patterns and custom colors I maybe missing other things.
I get you. (slightly off topic: sounds like something dblue should fix in his tool, instead of people trying to work around it?..)
Maybe but would be useful for automation in general.