Lost QCD check

No simple answer to this problem of lost checks, regardless of who lost them (US mail, IRA owner, lacks comprehensive guidance by the IRS or DOL (employer plans). Therefore, the treatment by different IRA custodians is not uniform. The custodian might have a stale dated check policy which voids the check after 6 months, or in this particular case payment is stopped and the funds restored to the IRA. This is not treated as a rollover, but when it occurs the custodian should correct the 1099R to eliminate the restored value. That may result in an RMD shortfall unless other funds RMD funds were distributed, and in the case of an intended QCD, there is no valid QCD if the charity was unable to negotiate the check and could obviously not provide the required written acknowledgement. The taxpayer will remain in the dark until the custodian’s handling is clear. If the RMD is not met a 5329 would have to be filed requesting the penalty be waived, the shortfall made up in the following year, and the QCD would also have to wait until the following year. The basic question is the same whether a QCD is part of the transaction or not, but the QCD adds another party to the problem.
If the custodian will not reissue the 1099R without the lost check deducted, the IRS will expect that the IRA owner report per the 1099R as issued, but without reporting the QCD that never occurred, so there would be no QCD and the RMD would be fully taxable except for any IRA basis recovery. Whlle the funds were restored to the IRA, they would also have been taxed, and when they are eventually distribution over again at a later time from the IRA, they will be taxed again unless offset by actual future QCDs.  Therefore, this solution is not equitable and therefore the 1099R should be revised by the custodian despite the fact that I suspect very few will do that.
There is such a variety of scenarios possible, with no common oversight, the general consensus is for the IRA owner to do QCDs early, to follow up for the written acknowledgement (knowing that it is possible to receive the acknowledgement and still have the charity lose the check), and stop donating to inefficient charities. Also limit the number of QCD checks and the number of receiving charities. This can be done while still donating the same total dollars, just consolidating the donations and thereby reducing the number of checks subject to loss.
There is an entirely different reporting scenario for QCDs done by IRA owner checkwriting, which is gaining in popularity. There is no 1099R issued until the check is returned to the IRA custodian bank, and it may not be known whether the charity actually received the check, or where along the line it was lost.

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