At least some of the letters are for correctly refunding some of the Underpayment of Estimated Tax penalty.

If you let the software calculate the Underpayment of Estimated Tax penalty, the software does NOT take into account (a) if the taxpayer is in a disaster area or (b) if the taxpayer paid the amount owed on their own before April 15th (unless you manually go in and change the date on the 2210).  Both scenarios result in the software calculating too large of a penalty, which means the taxpayer may be due a refund.