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Hierarchy script with condition

I'm new to hierarchies and I'm trying to solve a specific problem where I need to build in some additional logic into my hierarchy. So the scenario is based around project time entries. An employee is assigned to a manager and there may be multiple levels. I can create a hierarchy based on the employee table - no problem. However, if an employee works on a project that is considered "cross-department" I want to be able to break that type of work out separately in a hierarchical view of the employees so I can see my "cross-department" hours separate for my hours grouped by employee and their related parent. Any recommendations on how to handle the "conditional" part of the hierarchy?

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