…is this at all possible?
( at the same time )
One starting point could be versioning your patch, e.g. with https://github.com/
If you work in different subpatches it is perfect.
But the problem will still be, how to merge your two different versions of ONE .v4p-file. As there is no merge-tool which works with nodes yet, this will be quite difficult, too.
but perhaps the workaround with subpatches works for you?