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CRA automatically assessed me. Now I can't netfile?

I am a self employed freelancer. I had some health issues and was unable to file my taxes for a few years.

 I don't owe anything for these years as it was a rough time and I made very little. Since I didn't submit my taxes the CRA for some reason automatically assessed me for one year. Basically just a guess what I might have made without any deductions. They then said I owed $3,000 for that year. 

 I've been in contact with a CRA collections agent who advised me to just file my correct return and that would replace the automatic assessment that they did. CRA phone support has no idea what I'm talking about and offered no advice. I'm no longer in contact with the collection agent after I explained my situation last year. 

"Change my return" in CRA my account doesn't work for this year. 

 Is there someway to netfile this thing, or do I now need to mail this return in? If I mail it, will they even know what to do with it? Turbotax is just returning an error that I already have a 2016 return filed.

Thanks in advance!