Yes, I have seen this. What I do is instead of deleting, I un-check the "enabled" box.
When upcoming recordings are deleted, the log file is removed directly and does not show up in "failed" or "removed".
I usually have my autorecords set to "record all", so I guess it is expected in this case for the entries to reappear even if they were stopped or aborted, but I (usually) would prefer if they did not come back in this case.
I would expect that if autorecords were stopped or aborted after already starting, they would be/not be recreated according to the "duplicate handling" setting. But I am not sure how tvheadend could know your real intentions. For example, sometimes I will stop a recording in progress because I decided I do not want it. Other times I stop a recording in progress because I notice the actual program has finished 5-10min before the scheduled ending and there is no reason to record another 5-10min of commercials/filler. Other times (rarely) I have stopped a recording because it was not being decrypted properly and I wanted to restart it in progress after fixing descrambling issues.
Note: sometimes when I have had EPG problems, I deleted all the upcoming recordings relying on the fact they would be recreated when the new EPG data was received. So it is not entirely a bad thing.