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Back in 2013, the system was changed so that when a question was closed, any custom moderator flags on it would not be automatically dismissed. However, this seems to only work when a question is closed by non-moderators. Custom moderator flags are still automatically marked helpful when the question is closed by a moderator. This question is reporting that what was implemented back in 2013 has either regressed in one case, or was left incomplete.

I just encountered an annoying situation where I had flagged a question with a custom reason, and a few minutes later my flag was marked as helpful, because a moderator closed the question when going through the close vote review queue without ever seeing my flag. (The timestamp of the flag dismissal exactly matches the closing time and I have asked them personally whether they saw my flag.) Moderators do not see flags in review queues for normal users, and when a post is closed the flags are automatically dismissed, so it is easy for custom flags to be accidentally dismissed without ever being seen.

The only flags which should be auto-dismissed when the question is closed are close and VLQ flags. Every other flag type should require an explicit moderator action to specifically mark the flag either "helpful" or "declined".

Please don't mark custom flags as helpful when a moderator closes the question.

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    Does this answer your question? Don't auto dismiss custom flags on close – Ollie Oct 17 '20 at 14:31
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    @Ollie That one has status-complete. – Dharman Oct 17 '20 at 14:32
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    @Ollie Either the issue has regressed, or in 2012 the system was left such that closures by moderators automatically mark custom flags on questions as "helpful". So, no, this is not a duplicate of that question. – Makyen Oct 18 '20 at 1:06
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This is now per this staff response:

Thank you for reporting this! The closing functionality has been modified to make this work a little better.

When a question is closed, custom flags are no longer automatically marked as resolved. The moderator interface shows the flags at the bottom of the screen, which was easily missed. Moderators will need to mark each custom flag on a closed post as helpful or declined.

However, when a question is closed from the moderator dashboard, the flag will automatically be marked as resolved. On the moderator dashboard, it's much harder to miss a custom flag since it's shown right underneath the relevant post. Here, we will assume that the custom flag was seen and the custom flags will continue to be marked as resolved automatically.

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