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I noticed an odd change in my rep a bit ago and went to investigate the source - I figured if someone had downvoted one of my answers I would try to improve it.

I managed to track the change to a question that was deleted, but fortunately still in Google's cache. A user asked a question that wasn't clear and provided sample data but not the password for it. I left a comment to that effect with some general suggestions to solve the problem. Another comment was added after mine with futher advice on improving the question. Eventually it was flagged and closed as unclear, as asker never came back or made changes. Apparently it just got deleted, and for some reason that gave me -2 rep.

At the same time I discovered another question I actually answered (with no votes either way) had also been flagged, closed, and deleted. But I lost no rep for that. Further research turned up another case where I had both answered and commented (I think) that also had a rep loss I didn't notice at the time.

I could understand if a comment is specifically targeted and deleted by a moderator for reasons of content, etc. But it seems odd that one could be penalized for leaving a comment to try and assist on a question that ends up deleted. Is this normal operation, was the delete not done correctly, or is it a bug?

I dug around on SE Meta (whew, ~600 results using all relevant search terms) and found this Q&A which notes:

removed - Most often, the post was deleted (this could be any post you took action on, not necessarily a post you owned).

This seems to imply this is normal behavior, but that a penalty only applies to comments and not answers that are removed when a question is. Seems like a faulty system to me - penalty for flagging poor posts (can leave a comment) or trying to help improve a question that ends up not making it?

I'll acknowledge and would like to avoid anything along the lines of "it's only 2 points" or "it doesn't happen that often."

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If this is reproducible then I would say that it is certainly a bug, but it sounds like the evidence is somewhat anecdotal.

I make a lot of Comments, and have often seen the Qs & As that they are on deleted, but I have never observed nor suspected deleterious reputation changes like those you describe.

I'm reproducing the full dot point from the SE Meta Q&A you cited:

removed - Most often, the post was deleted (this could be any post you took action on, not necessarily a post you owned). Keep in mind that when a question is deleted, all of its answers are automatically deleted as well. This event is also used when a user is removed. Note that when a post gets deleted, the question's title will be shown in plain text to those who do not have access to view it.

I've done this because its second sentence effectively says that when you provide an Answer that gets upvoted on a Question that later gets deleted, or the owner of that Question leaves the site through self-deletion or removal, then you lose those upvotes.

I am not saying that this is what happened in your case, because a -2 more often indicates someone downvoting an Answer, but just wanted to clarify what that dot point is about.

Thinking a bit harder I think that the -2 could be explained by you having received a +2 on a suggested edit that was accepted (perhaps long ago), and that Q or A (or its owner) now having been deleted. That +2 is documented in the Help:

You gain reputation when:

...

•suggested edit is accepted: +2 (up to +1000 total per user)

I'm not aware of any circumstances where Comments are involved in changes to reputation points.

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    You're absolutely correct on both counts: Comments never influence reputation, and the -2 that we're discussing here was indeed the reverse of the +2 for a suggested edit on a question that was later deleted. – balpha Jun 18 '14 at 10:06
  • ah-HA! That's it - it was a suggested edit. The problem (with my research) is that with rep below 10k you can't see deleted posts or their history, so you have no idea what happened without a very good memory. Using a Google result cache (assuming there's still one there) you get a snapshot, but perhaps the wrong one. I didn't remember changing the post contents and cache didn't show me as last editor, but I now realize I had changed a tag. – Chris W Jun 18 '14 at 18:26

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