Another reason I like growing from seed. I don't have room to be growing shrubs.
I've been in the same position before. A huge mother, too many clones, not enough room. It's not a bad problem to have I suppose. Now other than the clone taken here or there my next crops are all in little vials and fit in a couple airtight containers.
I say chop that mother up into clones and do a SOG grow. Keep a few clones and reverse them with STS and pollinate a couple of the females and make hundreds of feminized seeds. Then just pop X number of seeds for however many plants you want to grow. Veg them and put into flower when you're ready. Then pop some more seeds so you have your next crop ready to go when you harvest. That's how I roll. And since I veg for around six weeks there will be a few weeks where I have nothing in the veg tent. Less work, saves on electricity, and it gives me a few weeks to decide what my game plan is for the next grow, what I'm growing, what crosses to make, etc...
You running out of space because you have a big mother plant, a bunch of clones, and a plant in flower isn't the end of the world. There are plenty of solutions. You just have to choose one. Good luck.