Everyone's going to come across needing to change rules for an existing cube with data. Historically what I’ve done is to simply edit the rules, save, then wait about 60 seconds+ for the rules editor to become responsive again while billions of gears are turning in the background.
When checking the server log, there was always a line item after a rule edit:
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TM1.Server TM1CubeImpl::ProcessFeeders(in 60000ms): Done computing feeders for base cube 'XXXXX’.
I run Unload Cube, then edit the rules file, what do you know:
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TM1.Server TM1CubeImpl::ProcessFeeders(in 78ms): Done computing feeders for base cube 'XXXXX’.