A spammer made several posts on Computer Science. I went straight to destroy the account. The posts had both spam flags and custom flags. After destroying the account, at least the custom flags remained unhandled (I'm not sure about the spam flags).
The posts that had custom flags remained in the dashboard, the flag indicator was still present when I visited the posts, and the flags were still marked as unhandled in the flagger's history (even after waiting a few minutes and reloading, so it's not just a caching issue, or the cache is insanely long-lived). In my moderator history I see no mention of these flags being cleared:
10 mins ago - no link available
Moderator destroys user - for id = 9314
Moderator destroys user - for id = 9316
We destroy users when there is nothing redeemable to come from their account. At the very least in this case, all flags against this account should be automatically marked as helpful. There's no need for moderators to review them and clear them manually.
I would go further and say that when a moderator deletes a post or causes a post to be deleted (via a spam/offensive flag, or by deleting or destroying the account), all the flags on that post should be marked as helpful. There's nothing left to salvage at that point. There are many of flags that need to survive closure (migration requests, sockpuppet warnings, request to speed-delete, …), sometimes even deletion by community, but I can't think of any reason to keep flags around when a moderator deletes a post or a user.