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She can't or doesn't give manual commands to the clones anymore or, IIRC, her condition drops below a certain threshold. That would be what qualifies as incapacitated.Define incapacitated though. Cus it can have different definitions when comparing our version of "incap" to their version of incap.
So either they incapacitate her without breaking her connection, and she just manually directs the clones, or the clones do it themself.