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/
