The following applies to timers set to record some form of "Rerun" or repeat episode:
Yeah, agreed, my observation has been that if it exists in your DVR My Recordings, it seems NOT to record again. However, if an episode would be recorded again after you have already viewed and deleted it USED to depend upon IF that recording "record" still existed in the Schedule past recordings memory. This meant that if that record still existed in the list of previous recordings, it would NOT record that same episode, but if that record had been removed from the list of previous recordings, then that same episode would be recorded. Each record of past recordings is removed by the memory reaching its limit of a # of past recordings with the oldest being removed to make room for the latest recording to join the list of previous recordings. BUT even shows that are NOT recorded or are SKIPPED are still saved to the previous recording lists as SKIPPED along with recordings that were not skipped.
This means that if you are like me and have A LOT of timers (between 80-100), each instance of that show related to your timers and NOT recorded are saved to the previous recordings listed as "SKIPPED." and this can number in the hundreds of new records being added to the memory of the previous recorded list in a matter of days--less than a week, so I can get an episode of a recording I deleted from MY DVR a few days ago and it records the same episode once again in just a few days if the re-run occurs again after that time. On the other hand, if you have a few timers, then that list of "SKIPPED" recordings added to the previous recordings list will NOT populate nearly as quickly, so you have a good long time before an episode you just deleted from your My DVR will record again, maybe months.
If you want, go to your DVR screen, select the "SCHEDULE" tab showing the list of recordings to come, but scroll UP and you will see only completed recordings or non-completed recordings. NOW, select the OPTIONS button, and the Schedule Options screen appears. Now, select "3" to reveal SKIPPED recordings. Some of you--who have a lot of timers--will see an HOARD of skipped recordings, and they take up a majority of the entries on the list and collectively consume that vast majority of the memory or number of places on the list that (at least on the older DishPro and ViP's) were in the 300 or there abouts--according to my poor memory--that the DVR refers to if--providing it does not exist in your MY Recordings--it should record an episode as per your "record repeats" on such timers.
Bottom line is that there is no other way to prevent the recording of a "rerun" or repeat episode that you have already deleted from My Recording in any "manual" way. It is all down to if the record of that particular recording still exists in memory as listed on the Schedule list. At least that was how it seemed to work on the older DishPro and ViP's, and still seems to be the case with all the Hoppers, as well.
It seems the H3 uses pretty much the same method as the older DishPro DVR's (and later trhe ViP's) with, at least to my observation, without much or any increase in the number of records on the "Schedule" log of past recordings that includes SKIPPED recordings.