Hi,
I filed an amended return on April 14, after my spouse and I decided to file separately. I don't owe taxes, but his morning, the IRS withdrew the total amount of the refund from my account. My return is also still in process, but I'll effectively end up with no refund unless I'm also refunded the erroneous charge.
I'm not understanding your question. Did you originally file MFJ? When did you originally file your return? You shouldn't file an amended return until your original return is fully processed and you receive your refund or your balance due is deducted from your account.
Please provide more information so we may help.
IRS withdrew the total amount of the refund from my account
Do you mean the refund from your original MFJ Form 1040?
That makes sense.
your refund, or amount you owe is on your new MFS Form1040.
You dissolved the MFJ return; your spouse now has to file MFS also.