The system automatically generates the message that "you MAY have to amend your 2016 tax returns". From what you are saying, you do not need to amend your 2016 returns. You included the 8606 and contribution / recharacterization with that return. You are ahead of other tax filers who did not take care of this correctly.
The distributions on the 1099-R's will include earnings from each account as well as your contributions. It does not affect the IRA contribution limits.
Since you have reported your contribution amounts for recharacterization purposes, the earnings are just part of the distributions from the Roth's to the IRA's which must be reported by your financial company.
