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The equation set
Qi = SUM Cij Vj
is valid when all Vj's are measured from some (any) agreed point of zero
potential. Given that specification, the Cij are functions only of
geometry. Changing the values of the Vj's (still measured from the same
"ground") does not conserve system charge in general, but preserves the
values of the Cij.
It is standard terminology in "circuit" equations (even static circuits)
to refer all voltages to some presumed "ground point" of defined zero
potential.