I think I've encountered this type of problem before with a forgotten exchange, I can't remember its name but I understand that problem really exists. One manual solution is this:
For instance, if they have $100 in ETH and want to withdraw $70, you can recommend them to withdraw $80 and empty their balance instead of leaving a temporarily non-spendable amount of $10.
You have to recommend the users to withdraw as much as possible all that they have and put a reminder that remaining funds might be at loss so they'll be forced to withdraw all of it. Well, this is for the manual part and reminder but technically, it goes to the devs part.
This wouldn't be a solution for a centralized exchange. Users have the right to withdraw whatever they want. A minimum or maximum withdrawal is just limited by the platform. But can't force them to empty their wallet. This problem shouldn't exist anyway. As I told above, OP needs an experienced wallet developer or exchange developer who can solve it. The fund should move hot or cold wallet entirely from the user's wallet and withdrawal call should happen from the hot wallet. Otherwise, it's quite impossible to run an exchange. That's the reason actually why exchange requires high fees than actual network fees.