He has been with a large franchise for several years but due to high fees is not renewing with them this year.

And you're going to pay 800 min to the CA franchise tax board no matter where the LLC is...

I am the one In Sacramento CA and Roseville CA.They are a franchise so fee's are different from office to office. 

In March 2018 I paid the required minimum of $800  fee to Franchise tax Board for the year 2018.

Do I need to file an AP-206 franchise tax exemption every year with the State of Texas comptroller, or do I just need to file the 1120-H with the IRS? 

I’m interested in knowing how many BP members have invested in businesses the way Ray Kroc did to franchise and in actuality create a real estate portfolio.

Because of the long arm of the California Franchise Tax Board and what they consider doing business in California, my LLC will be deemed to be doing business in California, since I'm managing the LLC from California, even if if the property is located outside of California. 

Do I still need to pay the $800 fee to the Franchise Tax Board for my 2017 Taxes?

And I think they’re a franchise business model anyway.

If you're managing from California, your KS LLC may be subject to tax in California as well as the Franchise Tax Board takes a broad interpretation of "doing business" in CA.