Our approach was very collaborative between several students. We have seen that only the first (co-)author(s) and the last authors of the short paper will be qualified for the joint manuscript. What should we do?

You have two options: 1. If the students have equal contributions. Then, they can be considered first co-authors on the short (and long) papers. 2. If the students developed some components of their approach together, but one student found a technique that led to a performance boost. I would suggest submitting two papers: one with all the team members as co-authors but without the additional component and another one with the student as the first author.