No it doesn’t affect the interest deductibility.

This remains the case where you have a savings account linked to your loan account as an offset account.

The savings account and loan account, while linked, are separate accounts.

While deposits and withdrawals in the offset account will increase or decrease the amount of interest charged to the investment loan account, the deposits are not repayments of the loan and the withdrawals are not new borrowings.

The use of the borrowed funds is not affected by the deposit and withdrawal activity in the offset account.