Forgive me - I'm a longtime lurker - but I do this stuff for a living and I'm pretty familiar with Nike's brand strategy, and without giving too many specifics, I can actually speak to this. It's sort of confusing, so bear with me.
Jordan Brand exists as a boutique brand within Nike's overall umbrella as a
"top-end, conspicious consumption brand" - Cuse typically falls these days under the auspices of what's called the "Nike Elite" tier, which isn't necessarily inferior but generally manifests itself in different shoe and apparel templates. (Confusing things a little, Carmelo is a Jordan Brand endorser, and several of his signature shoes have been released in SU-themed colorways.) Nonetheless, they're an important program in the grand scheme of Nike's college strategy and typically get custom designs (vs. color-shifted templates), as well as custom shoe colorways for players.
An important thing to understand about major NCAA endorsement deals is that they're wildly complicated and generally negotiated between a coach, an AD, and an institution; my understanding of the matter specific to SU is that Boeheim's own Nike endorsement contract (which predates the Jordan Brand spinoff by many years and, to the best of my knowledge, is handled by parties affiliated with Nike and not Jordan Brand per se) is the main driver in determining who at Nike gets assigned to the Syracuse account. I can't speculate offhand as to whether it might change or if Cuse might switch to Jordan Brand or a different account team entirely if/when Boeheim leaves, but Nike takes their account extremely seriously and has for many years. (I always liked the 80's-era anecdotes about Nike producing prototype Cuse uniforms in dazzle fabric vs. Georgetown uniforms in "weathered denim" to complement their respective styles.)
