coach, there cannot be a "contract" in use that the player signed.
If the player signed a MLB contract, then he is not eligible for college baseball at the DI level. So, the clause could not be in that contract.
There is no contract with a DI, it is an NLI and MLB will not recognize any language in an NLI. MLB has the rules about the draft and they aren't full of loopholes and you cannot have a contract with a school or the NLI that gives you any leverage with the draft.
To illustrate, Rice had a pitcher drafted 2 years ago. Not signed during the summer. He went to class but said he would not play college baseball. He asked MLB to waive the provision and allow him to continue to negotiate with his drafting team. MLB said that upon returning to school and enterring the classroom, the player lost his draft eligibility until the next year he would be eligible, whether he plays or not. So that player lost both in the draft and forfeited a college season.
There isn't much wiggle room here. I think there might be some misunderstanding of what happened in the situation you describe. Based on that player going to school, he lost his ability to sign until he is again draft eligible whether he played in college or not.