Normally you are not allowed to change from a joint return to separate returns after the original due date of the return. "Separate returns" means anything other than joint, including single or head of household, not just married filing separately. That's why the IRS told you that you cannot amend from joint to single. But your situation is an exception to the general rule, since you were not legally married on December 31, 2018. Your joint tax return is what is called an "invalid joint election." You can and should amend the incorrect joint return, but a special procedure has to be followed, and there are complicated rules for additional information that has to be submitted with the amended return.
This is a very uncommon situation, and it's a very obscure part of the tax rules. I recommend that you have a tax professional prepare your amended return with the attachments that the IRS requires. You probably won't find a tax pro who is familiar with this particular situation - it doesn't come up very often - but look for someone who has experience dealing with the IRS in unusual cases. You can tell the tax pro to refer to IRM 220.127.116.11.7, which is the section of the Internal Revenue Manual (IRM) that covers an invalid joint election. When you meet with the tax pro, bring copies of your original joint tax return.
To get your amended return accepted, changing the filing status from joint to single, you have to first of all clearly state that the original return was an "invalid joint election," and explain the circumstances. Since this is such a rare situation, I would also suggest that you reference IRM 18.104.22.168.7. The tax pro will know how to word the explanation. IRS procedures require two things in order to accept the change of filing status.
1. Documents verifying that you were not married as of December 31, 2018.
2. An allocation of all "income, credits, and payments" on the joint return. "Allocation means the taxpayer must designate/show which wages, deductions, withholding, EITC, tax liability, etc., belong to each taxpayer." Here's where you really need a tax pro. There are very detailed rules in the Internal Revenue Manual, IRM 22.214.171.124.8, about how to do the allocation.
This is not something that's covered in normal IRS instructions or publications. If you want to look at the applicable sections of the Internal Revenue Manual yourself, go to the following link. The Internal Revenue Manual is the manual of procedures followed by IRS employees. It's written for them, not for taxpayers, so it is addressed to them and assumes a level of knowledge that they have from their training.
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