Do I report a 1099-R as taxable income where the IRA custodian sent a QCD from my IRA to a charity and issued a 1099-R but the check was never deposited by the charity?

As you are aware, if the funds never made it to the charity, it isn't a QCD.

If the funds are back in the IRA (or never actually left the IRA because the check was voided), you would either have to ask the IRA custodian to correct the Form 1099-R to reduce the amount in boxes 1 and 2a by the amount that was never actually left the IRA (I suspect that they would be reluctant to do that) or you would have to report the amount as a as having been rolled over to an IRA (using self-certification that this would qualify for a waiver of the 60-day rollover deadline) .