Your federal tax due cannot ever be paid from a state refund. So you do not have to worry that anything will be deducted from the state refund and go to the IRS to pay your federal tax due. That is impossible.
And...especially if this was your first time to use the CD/download and encounter the state e-file fee, it can be confusing. You can avoid the $25 state e-file fee by printing and mailing the state return. If you choose to go ahead with e-filing the state and just pay the $25, you really do not want to get suckered into saying you will pay that fee from a federal refund (which in your case was not an option---but for many users it would be) because that will get you an extra "refund processing fee" of $39 or $45 (in CA) added to the fees.
TurboTax shows you a summary that nets out the difference between the federal tax you owed and the state refund you are going to receive, which likely led to your worry that some of your state refund will go to the feds. But....that will not happen. You should get your state refund in total.
To track your state refund:
https://ttlc.intuit.com/questions/1899433-how-do-i-track-my-state-refund
https://ttlc.intuit.com/community/state-taxes/help/how-do-i-contact-my-state-department-of-revenue/0...
**Disclaimer: Every effort has been made to offer the most correct information possible. The poster disclaims any legal responsibility for the accuracy of the information that is contained in this post.**
