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After you file
@townrun I spoke with the IRS yesterday (May 3, 2021) via their toll-free number, and their instructions were just as @macuser_22 said at the beginning of this thread. The primary taxpayer listed on the already filed MFJ return needs to amend theirs to MFS, and the secondary taxpayer needs to file a new return as MFS. In addition, the secondary taxpayer will most likely need to file an extension as they cannot file until the primary taxpayer's amended return has been accepted; an approximate 16-week lead time as of My 3rd. This is the exact scenario my spouse and I are going through and I needed to get clarity directly from the IRS.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**