I would:

1. Amend the tax return to remove the dependent elderly mother.
2. Respond to the IRS notice telling them the dependent is being removed on an amended return (you may even include a copy of the soon-to-be-amended tax return with the response to the notice).
3. File elderly parent's tax return.  She will still be disqualified from the Premium Tax Credit (because she qualifies to be a dependent), but the repayment will be much lower.