First, you should respond to the FTB by the deadline date given you. This is very important.
As for your 2018 refund(s), it's doubtful that either refund will be affected by this notice from CA FTB. Typically, if there is past tax due, the state will send you a payment notice separately after your case has been finalized. That may take some time. If you end up owing more tax for 2016 than you paid, you'll be given the opportunity to make payment when that has been determined. If you DO owe taxes from 2016, it's best to go ahead and pay as soon as possible. Interest is being accumulated on any past-due taxes.
*** I am NOT a tax expert. I am a seasoned TurboTax user, and volunteer to provide assistance to TT users. Nothing I post is to be considered TAX ADVICE; I bear no legal liability for responses.***