If you're referring to having multiple roots, there are two solutions:
(a) define your 3-way-merge primitive (the non-recursive version) to support merging two states against an imaginary "zero" that acts as the single root. So in the counter version you can imagine that everything "actually" starts from 0.
(b) arrange your application so there are never multiple roots. In some cases this not really a constraint, usually one single person starts a document and it doesn't make sense to merge something else in later. In some other cases (group chats, tree histories like git) this is probably not acceptable and you will need (a). But in the examples I just gave, a reasonable (a) is fairly straightforward to think of.