When an individual owns the same security in multiple trading/brokerage accounts, adjusted cost base should not be calculated separately for each account. It may seem as though you should calculate adjusted cost base separately for each account, but the Canada Revenue Agency (CRA) requires that it be calculated jointly, as if all brokerage accounts were merged together.
If you own the same security in both a taxable account and registered accounts (RRSP or TFSA), any transactions within the registered accounts are non-taxable and thus ACB does not need to be calculated for the registered account. The transactions within the registered accounts can be ignored when calculating ACB for the taxable account (with the exception that a transaction in a registered account can trigger the superficial loss rule for a transaction in a non-registered account).
AdjustedCostBase.ca provides a feature that allows users to have multiple portfolios. However, separate portfolios should not be used for the case where you have multiple personal non-registered accounts. It should only be used in other circumstances, such as for tracking ACB in a corporate account, or when using the tool for family members or clients.
This may be part of the reason why brokerages are not held responsible for reported ACB to their clients. Since the brokerage is unaware about the client’s other accounts, it would be impossible for the brokerage to provide information on adjusted cost base to the client that’s guaranteed to be accurate.