The IRS knows all of your investment balances on Dec 31 along with your RMD for each account. The IRS allows you to remove the money from one IRA account and their computer will do the math work. It is actually a system that works well.
Of course, you should keep your end of year statements and how you determined the RMD with your records.
I am certain you marked all RMD or you would have had more trouble and questions for us.
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