Per this post from Jeff, the Very Low Quality flag:
The VLQ flag now carries a downvote from community. It is like "spam flag lite", meaning, no reputation penalty but like spam, it incurs a downvote from the community user.
If a post is edited, any pending VLQ flags are now cleared (without harm) from the post. It is unclear that a post is still VLQ if it has been edited since it was flagged.
I am not sure if #2 is applying to PostLowQualityAuto flags. I was able to reproduce this by
- Clicking on the link in the flag listing.
- Editing the post (in my case it was an answer, see https://drupal.stackexchange.com/a/78282).
- Dismissing the flag as helpful
When I dismissed the flag, the score remained at 0, but when I refreshed the page, it went down to -1.