There's a bug in BPIP:
Hey @Vod, is there any glitch in the merit stats?
Yes, I am hunting down a bug that will sometimes give a merit to the wrong person... :/
Could this be the cause? Or did you see the number of Merits go down in the profile on Bitcointalk?
The BPIP bug(s) that Vod is hunting down, outlined above, seems to be referring to a different phenomenon from the situation that I described, which is whether merits are subtracted if merited posts are deleted..
It seems that your understanding (LoyceV) and mine are the same. The merits should not be deleted, so it seems to me that the jury is still out about whether there are circumstances in which merits might be deleted (along with deleted posts) beyond extreme intervention abuse situation that seem to be exceptions and had been previously mentioned, as extreme case exceptions, by theymos.
This iasenko investigation seems to explain the situation - while simultaneously pointing out unresolved bugs of a different nature from the original question.