It is 39 Year property. 3K of depreciation makes 117K the office basis, which if it was 10% of the home it gets you to a 1.2MM home. Plausible. 3000 square foot home with a 300 square foot office? 7K of expenses does not sound like such a stretch if the home is worth that much, especially if there is a mortgage on it. Not sure about IL property taxes, but again, if the home is worth that amount, the tax bill is not cheap. Not saying these are facts, just making an observation that everything is plausible.
If you wait until you file the 2024 return, you could slip in a 1310 and get the depreciation back....that is not the correct way to do it, you should amend and notify the plan administrator of the corrective distributions needed and pay the penalty for the excess contribution. You will get a 2024 1099R from them that includes the earnings.
Tom
Longview, TX