I've done that. However, I got one 1099-R for multiple years of excess Roth IRA contributions withdrawn in 2018, with different distribution codes identifying the years. I know I have to pay 2 yrs of penalty for the 2016 excess contribution. The Roth Custodian did not determine taxable income for 2016 and no tax withheld (box 2a and 4 are blank for distribution code J), so I have to figure out and pay all that with Form 5329 according to my Custodian. I assume that gets filed with an amendment 1040X for 2016. But since I earned something on the 2016 excess contributions in 2017 also, I am wondering if the 2016 excess requires amending 2017 taxes.
