What brings about their differences? If dimensions then that may be a limiting factor. Do they use differing chemistry?
If you do not know the answers to those questions etc. it might be better to stick with the original capacities and voltage.
That said if replacing cells in the original battery case using the original control board I would suggest you investigate whether that control board will permanently switch something to open circuit if it sees no voltage or too low a voltage, at any time.
It might be necessary to either
1) rig up a connection, that is independent of the cells, that will supply the board with the needed voltage whilst the actual cells are being swapped. Or,
2) if such monitoring monitors each cell individually, connect the new cell in parallel with the old cell BEFORE the old cell is disconnected.
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