You can split the models/NWCs up by level or use search sets to only clash levels against levels. I typically clash all levels at once on most of my projects and mark any clash groups on levels I am not currently working on as "reviewed" and assign "Level 04" or "Future" to the clash group. Then in Navisworks 2026, you can simply filter those results out. The Clash Grouper also really helps for grouping clashes by floor.
The areas are a little more tricky since there's nothing in native Navisworks to do this but we use a 3rd party plug-in called Flypaper Sherlock to create areas within the NWF. Unfortunately, they were recently acquired by Procore, so I don't believe you can purchase a stand-alone license anymore.
Feel free to DM me if you'd like more help. I've been doing advanced Navisworks clash tests and search sets for at least 8 years now.
