because what happens is the bigger one takes over the other ones roots.
This is incorrect. One plants roots will not take over the other plants roots. Only parasitic plants do that. What will happen is that the roots will intertwine and grow together, and the more vigorous one will take over the pot leaving the smaller one stunted since it is getting less soil/water/nutes/air etc.
Look up a little bit about bonsai and you will realized that as long as the plants are past the seedling stage there will be not problem in cutting the plants apart. Don't worry about cutting roots, it will happen. If you can separate the plants, then by all means do it. If not, don't stress. I've replanted mothers in the same pot w/~75% new soil and didn't lose any of them. To the contrary, if the plant is root bound severely, they will show their appreciation for the new dirt w/lush green growth
Did the two plants come as one seed or two seeds/cuts. If they are seedlings from the same seed, it will be much more tricky as the roots will be intertwined much more, but if it was two separate plants planted on opposite halfs of the container, then I wouldn't worry a bit about performing the surgery.
Be safe and hth
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