In my opinion, this error message displayed is unclear. What it means and does are different.
I often do the same (save as) and receive the same message-having no problem. There may have been an auto-recover file saved in your specified file location (depending on you save settings - interval and location), but I find that the in-context parts that this message is warning of, do not have reference problems.
You can choose to keep the autorecover files, or delete, depending on your comfort level of your file structures.
This behavior is there in 2014 too. I think it's stupid that they don't just give you an option to update the references to the newly saved assembly.