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I've been having various X1 DVR issues for months ... currently working with the Comcast team to resolve them.
You may need to try several times to delete the program ... sometime 20 or 30 tries, but it should eventually delete. Do not restart the box. Instead hit the exit button and try to delete again. As mentioned, you may need repeat this a ton of times, but so far I've always been succesful in deleting. You can also try syncing the DVR under the device options menu while trying to delete. I've found that may help as well.
Did you try pulling the power cord from the back of the X1 box and plug it back in?
It's almost definately a back-end or back office issue that will need to get fixed by the advanced level support. Swapping equipment will not help, but you may need to do that as part of the troubleshooting.
I was seeing all sorts of strange X1 issues for months ... old recording reappearing, new recording disappearing or deletion issues, old equipment still showing on the X1 guide. Equipment swaps didn't help.
Eventually it got escallated to a high enough level that an engineer was assigned to my ticket. My fix is ongoing but it looks like it's related to back-end account issues somewhere and I've seen a lot of improvement.
If you're able to get a ticket # for your issue, you may need to be persistent and try to get the ticket escalated, and possibly swap equipement just to prove that's not the issue. BUT, there should be no need for a tech visit.
I fixed it. To correct this you need to fill your Cloud DVR. I recorded enough programs last night to fill the 60 hours available on the cloud DVR. Once it got it full it purged the stuck recording automatically. The stuck recording was the oldest so it deleted first.
There is a risk you purge a recording you may want, but this will not delete your local recordings on the box unless your local DVR storage is full.