If there are penalties / overdue fees / etc. - one can still send the reply letters to the IRS (even if past the 72 hour reply window) and send proof of lawful money redemption (even recent checks dated from 1-2 days ago). Students have seen the IRS relent once this has been sent, but it is not a guarantee of success for prior issues that occurred prior to redeeming lawful money (see statement above).
Remember to always approach the IRS with non-adversarial language. One must not appear as a tax protester e.g. "If we owe something, we'll pay it, but we're asking if XYZ is correct." That is not tax protester language, it's "being a good accountant" language. One agrees to pay what is owed, but simply is asking for proof. This cannot lead to further "Frivolous Argument Penalties" from the IRS - it's simply asking a question and telling them if it's correct, we'll pay.
Finally, one can tell the IRS "If I had known about lawful money redemption, I would have done this for the prior 7 years of filing." It has a (low) chance of working - but one must be focused on simply settling all issues with the IRS back to ZERO (no fines or overdue fees). Count any money paid into the system as "gone" and live life correctly from now on. If one tries to fight the IRS on taxes paid in... buckle up for a wild and scary ride! It sucks to hear this, but it's the harsh truth we've seen play out 100+ times with so many students who fight taxes paid into the system.
NOTE: Can one really think a vicious and unforgiving government would ever let go of funds given to them (even if it was taken by deceit)?