Is it permissible to withdraw the deceased father's bank deposit, or to leave it there, after realizing it is unlawful?

The benefits from investment certificates are usury (riba) and unlawful (haram). What your mother did by placing money in a usurious bank is legally forbidden (haram shari'an). It is obligatory to withdraw the money immediately and dispose of its profits through charitable avenues, such as giving them to the poor and needy. The difficulty of living expenses is not a justification for persisting in falsehood. There is ample permissible (halal) provision to avoid the unlawful (haram). Therefore, the deposit must be dissolved and withdrawn.