We just renewed their lease in August, with what now seems like a mere pittance (.06%).                                                          

Leases are already in place with national tenants and many are for 20 years with many renewal option.

Also they typically charge points, 2-3, for renewing for additional 4-6 month terms.

The renewal fees for the license itself are peanuts.

Otherwise, you should go with what your lease says and probably consider not renewing them in December. 

This could include, for example, renewable energy such as solar, which would allow tenants to pay those utility fees to you rather than the power company.Also, consider furnishing your properties, so tenants are willing to increase what they’re paying to rent in exchange for the furnished property.Want To Ramp Up Your Rental Income?

Landlords may remove option of automatic renewal to  month to month once lease term expires.

At that time you could try and renew with increased rent or look for new tenants.

I could be wrong, but either way, I'd refuse to pay it.Archiving records is the cost of doing business, just like license renewal fees, E&O, CE courses, etc.

It is up to you if the late fee they are paying is worth it/sufficient.If you are not depending on timely payments (for example, if their rent is not paying your mortgage on the property), I say take the additional late fee income (I hope your late fee is substantial).When their lease comes up for renewal you might decide not to renew, you might leave rents the same or increase to whatever the market commands, but if you do renew I'd probably increase the late fee or restate your late rent policy to whatever you are more comfortable with.Keep in mind that charging a late fee does not prevent you from filing eviction.