Account 1: Owner A and Owner B
Owner A conducts a $100 cash withdrawal

Account 2: Owner B and Owner C
Owner C conducts a $10,000 cash withdrawal
(Funds from previously deposited check in Owner C's name)

Owner B did not conduct either cash withdrawal, was not present, and we have no knowledge that she is benefitting.

Am I correct in thinking I do not need to file a CTR?

If you have no knowledge that either withdrawal was made on behalf of Owner B, you would have no person on whose behalf more than $10,000 in cash out transactions were completed, nor would have have any individual who conducted transactions in excess of $10,000.

Therefore, you would not need to file.

A cautionary note: If your bank has a stated policy or procedure that it will, when aware of facts such as those you've described, consider that the transactions are conducted on behalf of all co-owners, you'd have to file due to the policy or procedure, since it is also acceptable under FinCEN's CTR FAQ guidance to assume that both withdrawals from and deposits to joint accounts are on behalf of all co-owners. In that case, you'd file a CTR listing Owners A, B, and C, with box 2a checked on Owner C's portion of the filing, and box 2c checks for Owners A and B.

And, FWIW, the source of the deposit to Account 2 is irrelevant.