HQ never has rare materials

[Skyrim]

I have multiple rare materials plots in different settlements and there are still no rare materials at HQ I also have caravan plots at the settlements

 

[SarahAda]

So if your virtual storage is full, new materials won't displace old materials. is it possible you have a bunch of building materials industrial plots that are filling up the storage?

if this is the case, consider adding new storage containers to let the rare materials flow in, and you might also consider Sim Settlements 2 Excess Resource Manager which will automatically sort and dispose of materials you don't need to keep your production running.