we do have a minimum fee that is $3k/year which at our fee structure means a project has to raise about $35k to cover that minimum.
Originally a driving factor was to determine the minimum size project we want to work with and then create a minimum fee tied to that. This helps de-incentivize super small projects from wanting to work with since our minimum fee would then make their effective rate high.
At the end of each year we would look at how much they paid us and if its less than $3k we would bill for the balance.
That said - now I really work with orgs with bigger budgets (closer to $100k minimum) but we have not raised our minimum fee.
Furthermore, we also have projects pay a fixed rate/month to help offset our insurance costs. This does not cover our services really but it at least gives projects who are not active at all a reason to want to leave since they are essentially just burning through funds each month paying for insurance.
Hope that helps, happy to chat more if you want to!