Some site users have noticed old comments being deleted. This is correct - site comments are meant to be a mostly temporary means of improving questions and answers. Here's an explanation of the process we use.
Argumentative comments or extended discussion comment threads hijacking an entire question/answer will get deleted semi-immediately. Take it to chat or meta. What is "extended discussion?" If the comment thread takes up a whole Web browser top to bottom, you're definitely there. If you can't see any answers from the bottom of the question - you're there. Comments criticizing the content of a question/answer are fine; point by point rebuttals are not on topic here. If you want to write something really long, write your own better answer.
Answers in comments - on the question, normally - get deleted immediately. Posting an answer as a comment is simply an end-run around the usual community voting, editing, etc. system and is inappropriate. (Further reading: Should users refrain from answers (or partial answers) in comments?)
Obsolete comments - like "What about X?" "Good question, I edited that into the answer" get deleted as they are seen, as they have achieved their purpose. This is a happy deletion - job done, time to tidy up. Comments suggesting changes get tidied up after a while too if the post author rejects the suggestion.
Trivial comments - like "+1! I like that idea!" get deleted eventually. My preference is to let comments like that stand as part of the collaboration around a question, as they do provide helpful feedback around the whole process. I don't touch those until initial activity on the question has dropped off and it's clearly become part of the long tail of questions. Then, I'll delete a comment like that when happened upon. When an old question pops up or I'm going to it, I'll delete comments that fit this criterion. (Needless to say, this is what voting is the persistent implementation of.)
Irrelevant or pointless comments - like most jokes - same thing; deleted once a question quiets down. Happy to let them go while the initial stampede is on, but no sense burdening posterity with them. If there are so many that it's taking up a page of real estate and hiding real answers, they may go quicker.
Lengthy discussions, similarly, are discouraged and will be cleaned up once a question quiets down. Important information or clarifications should be rolled into a question or answer, not left in ten back-and-forths. I sometimes put comment-notes at the end of these saying something like "Please incorporate any useful info from this into your answer, for this comment thread will be cleaned up soon."
Of course comment deletion (and editing valuable info from them into the real question or answer) isn't just up to mods, please do it with your own Q&As, with others' if you have enough rep, and if not you can flag comments for attention. Like so...
If we get flags on comments, we will act to delete more quickly than usual because it's clearly bugging a site user in a non-hypothetical way.
Needless to say, comment deletion isn't binary. If comments seem to have lasting worth, and lots of upvotes on them is part of that, they get left. We don't get charged by the comment so we're not obsessed with deleting them all. We do, however, want questions and answers - individually and as a whole thread - to be easy to read and understand, and extensive commenting hinders that. So the best thing is for valuable info in comments to make their way into the Q&As, and for low value comments to be deleted.
As some explanation as to why this is a SE practice and not just "the Man trying to keep you down," I submit for your approval a statement from Robert Cartiano, Director of Community Development for the Stack Exchange Network, who says here on an equivalent question:
It's no wonder users are taken aback when Stack Exchange works against their spirited debate and conversation. Before Christianity SE, "traditional" discussion forums taught us to jump into the fray of the witty and insightful discussions where you could bounce off off into ever-branching sub-conversations as easily as you could click and type.
The problem is that most online discourse reaches noise levels reminiscent of a group of friends at a spirited get-together. Stack Exchange specifically discourages that type of debate and on-going discussion. That is by design — but to understand why comments are so transient and expendable, you have to understand the core purpose of Stack Exchange's behavior. Stack Exchange in a Nutshell
After someone asks a question, members of the community propose answers. Others vote on those answers. Very quickly, the best answers rise to the top. You don’t have to read through a lot of discussion to find the best answer. If an answer can be improved, users can edit the post.
Comments help facilitate that wiki-style editing by allowing us to ask for a bit of clarification or otherwise help improve that post. That's what comments are for. Period.
When users start adding important, useful, and interesting information in the commentary, you break down that structure of "one question, best answer." You have to comb through all the commentary for import addendums and corrections and partial answers and important bits of information spread throughout. That entirely defeats the purpose of having a Stack Exchange site on Christianity.
It's not enough to say that your comment is just harmless banter that isn't hurting anything. Users will imitate what they see, so when they see conversations posing as answers, they'll follow with their own… and the problem propagates.
There's nothing inherently wrong with communities that that want free, open-ended discussion and back-and-forth debate. If traditional forums are your choice, there are certainly enough of them out there.
But on Stack Exchange, routine cleanup of comments helps enforce the purpose of comments. Comments are there to discuss improvements to the post. When their purpose has been served, they are deleted. When comments drift into conversations, they should be deleted. It's all part of discouraging comments from becoming mini chat systems…
… and for users who have been around long enough to see how well this system works, it is a welcome change.
Is this practice clear and understandable? Is there any additional guidance we should take into account when handling comments?
Addendum: Comments on meta are not deleted (except for cause); meta is deliberately more discussion-y than the main site. This seems to be causing confusion for many posters here so I thought I'd address it directly.