Prioritization and scheduling of work are related, but keep in mind, I’m not talking about prioritizing stories. We’re talking about a higher level than that.
The fact that people are working on a 2 week sprint model, may itself be part of the problem. Is the sprint the thing you optimize for, or is it the work that needs to be done within or across sprints that should be optimized.
In many companies, the rigidity of these work models runs VERY much counter to what it should mean to be “Agile”.
When it comes to “work”, that should start with those higher level priorities, and the goal is to bring those to reality. Other tasks can be folded in and scheduled (I won’t overload the word prioritized here) to support those key priorities.
There’s no magic formula here, but if everyone is aligned on objectives, then decisions on what to schedule and what not to schedule become easier to make.
IF there are still major issues about scheduling then clearly there is a disconnect WRT real priorities and those should be resolved with the broader team, including Execs if needed.