One of my 1099 R forms was included twice in my submitted 1040 and 540 forms. Do I have to file an amended return?

Yes----information flows from the federal return to the state return so you must have entered the 1099R twice on your federal return, thus affecting federal and state returns.  Wait for the returns to be fully processed and amend both your federal and state returns to delete the duplicate 1099R income.

See this TurboTax support FAQ for amending a tax return - https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-change-correct-return-a...

https://ttlc.intuit.com/questions/3827521-can-i-efile-an-amended-state-return

 

 

Do not expect quick results from amending. It can take four months or more for the IRS to process an amended return.  

 

You can watch for information here:

https://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1

 

 

You should be able to contact the FTB, explaining that the 1099-R was entered twice by mistake and they should be able handle the change on their end without amending.

If the FTB sent you a letter which included a phone number, then contact them using that phone number.

If not, then go to this FTB website for how to contact the FTB - https://www.ftb.ca.gov/help/contact/

If the FTB handles the adjustment without an amended California tax return, you still have to file an amended federal tax return to make the correction for your federal tax.