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Normally - it takes about 1.5-2 years for the IRS to realized that no tax return was filled and send a notice about tax liability...
If the form 1099-misc is not reflected on your tax account - most likely it was never sent or was sent with a different tax identification number.
Since you received forms 1099-C from your employer - it is very likely that these forms were sent to the IRS as well - please verify what tax ID was used on these forms?Did you provided your business tax ID instead of your SSN? - it is possible that forms 1099-misc were issued with your business tax ID.Please verify.
There is no magic - if your employer did not send information under your ID - that information would not be in the IRS computer.
Most likely your accountant knows that - you need to use form 4506T - www.irs.gov/pub/irs-pdf/f4506t.pdf to obtain your tax account transcripts - not form 4506.
On the form 4506T - check the box 8 - Form W-2, Form 1099 series, Form 1098 series, or Form 5498 series transcript. The IRS can provide a transcript that includes data from these information returns.
Also the box 6(a) should be check d for Tax account Transcript.
I suspect that your employer did not issue forms 1099-misc to the IRS - and that was the reason they required to have a business entity.
That is why your income information is not in the IRS system and you never received any notices.
Please be aware that according to the tax law - you are required to report your income regardless if it was reported to the IRS or not.
So technically speaking - the fact of not reporting should not affect your filing requirements or tax liability.
Unfortunately based on very limited information - there is not much we could say.