What is the ruling on dealing with an Israeli software company, knowing that its nationality was discovered after beginning to deal with it, and is it permissible to withdraw the money accumulated from it, and how should it be disposed of?

It is permissible for you to deal with the company as long as the transaction is carried out as described and does not involve promoting something forbidden, and you are given a specific commission for each download of the program. If it is proven to be Israeli, it is not forbidden to benefit from the commissions paid in exchange for a permissible benefit, but you must stop dealing with it in the future, in accordance with the principle of boycott decreed by a group of Muslim scholars.