Short answer - yes you can file them out of order. But.....
Filing out of order will trigger a red flag and they will go insearch of your other returns and possibly making their own return for you. In addition ff you have any assets and you file out of order depreciation will be a pain and you may miss out on additional monies owed to you and possibly have to file amended returns to recoup, causing possible additional red flags. All of which will give you a big head ache and added stress no business owner needs in their life.
Best advise go to a local CPA and have him file starting with the 2016 returns. If they are filed close together any money you are due a refund from the later years will auto apply to your previous years.
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Thanks. I was having a hard time finding a cpa that I could trust to do it right. This is a good info to have when dealing with this lady. She seems knowledgeable though. I just don't want issues with the red flags like you said.