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The proper way to file Form 5329 is attached to Form 1040, or to  Form 1040-X.
Form 5329 can be mailed by itself only when you are otherwise not required to file a tax return.

 

If you already mailed 2024 Form 5329 alone, I can't tell you what IRS will do with it once you e-File.

 

@operaflute