You should have only taken credit (for the Retirement Savings Credit, for example) for the net actual contribution to your Roth IRA - in other words, your original contribution minus the excess contribution that was returned to you.
You should have reported the excess contribution that was returned to you on line 15a of your 2017 Form 1040. You should have reported the net income attributable (the earnings on the contributions while they were in the IRA) on line 15b of your 2017 Form 1040. You should also have included an explanatory statement. You should also, if you were under 59 1/2, paid a 10% penalty on the net income attributable via Form 5329.
Even though you received the money in 2018, the IRS is very clear that the earnings are treated as taxable income for the 2017 tax year and should be reported on the 2017 tax return.
For all of the items in the previous paragraph, you can read about it directly in the 2017 instructions for Form 2017, page 5, middle column, "Return of IRA contributions" here:
https://www.irs.gov/pub/irs-prior/i8606--2017.pdfFor all of those items in the second paragraph, you will need to file an amended return for 2017. This will be a Form 1040-X, plus you'll need to add Form 5329.
In other words, the Vanguard CSR with whom you spoke in February 2018 was mistaken. The Vanguard CSR with whom you spoke yesterday was correct.
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The 2018 1099-R should have on it
all of the earnings attributable to your excess contribution listed on it. It should include the excess earnings from the entire time from your original contribution in 2017 to the withdrawal in February 2018. I don't believe that you will receive a 2019 1099-R because there is no need for it. You can confirm this by comparing the numbers on the 1099-R with the amount that was returned to you in February 2018 - they should match exactly. BTW, "PJ" is the proper set of distribution codes for the circumstances you describe.
HTH.