I use cash basis accounting and this is not my first year in business. I freelanced for the company for 16 years.
I like your Option #1--Get the payer to issue a corrected 1099 if the first one is incorrect.
Since I have not yet seen the 1099 (although I know a check was cut and never mailed), I don't even know for sure if I have a problem. I have sent the CEO an email asking when I will be paid and looking for reassurance that my 1099 will match what I've ACTUALLY received. I have not yet received an answer.
It was a small company, so I have lots of emails back and forth with the CEO fully documenting the fact that they were a "slow pay" for years and that I was not paid for my last project. I would have little problem documenting my case if I needed to.