If a post has a low quality score flag on it, it's automatically dismissed as helpful if a user edits it, which results in an automatic Community downvote. I understand (kind of) adding a downvote if a moderator marks the flag helpful, but it seems bad to downvote the post at the exact instant somebody edited it to fix the problems that resulted in the flag in the first place. Either the edit should dismiss the flag and not cause a downvote, or the flag should stay around until a moderator has looked at it, regardless of post activity.
The system will now revoke the automatic downvote if, after the flag is marked Helpful, the post later gets an upvote.
Remember, the automatic downvote essentially exists because folks use this flag in cases where they should be downvoting. As such, it serves an important role... But should still be considered weak compared to actually downvoting the post in cases where there is conflicting information.
A situation where the post isn't actually deleted (either because the post was edited or because it was simply undeleted) and goes on to attract positive feedback is clearly a situation where the flag itself is weak signal, and it no longer makes sense for the system to impose an automatic downvote.
I think this serves to address both the scenario you've identified and also the scenario where a VLQ flag results in deletion via /review/low-quality which is later overridden by the post's author, trusted users, or a moderator.
Update: As of August 15, 2019, the system no longer casts automatic downvotes as a result of automatic low-quality flags being marked helpful.
Personally, I think the edit action should dismiss the flag as disputed, which is actually what it did for a long time and I thought it still did. I was never able to figure out when the change actually took place though.
There are other questions on Meta (one from August 2012 and another from August 2013) that suggest very low quality flags did get dismissed as disputed, and for quite a length of time from the looks of it. I'm not just imagining this. I don't understand why it was changed away from that.
It really doesn't make sense to dismiss these as helpful. A very low quality flag in itself is saying this post is not salvageable. Yet by editing, I'm saying it is salvageable - look, I'm salvaging it right now! I realize that it's prone to abuse by users who are just editing to dismiss the flags but: a) A user never knows their own post has been flagged as low quality, so they'd just be editing as a guess that they might have one and b) dismissing these as helpful doesn't really damage the user abusing this method anyways. So they got a downvote, so what? The flag is still dismissed, which means if it really is low quality, it won't get deleted like it should. So really we're only punishing the people making legitimate edits.