We've organizations with path A1 → B1 → C1 and A1 → B1 → C2.

I have to know which a part of path forms entity group. Is C1 and C2 goes to entity number of A1 → B1 and A1 is separate entity group or there's just one entity number of A1?

Organizations form groups according to roots of the ancestor hierarchy. Different root means different groups. So inside your situation, you've only one entity group since individuals two pathways you've pointed out are generally rooted in A1.