On a few occasions I have disagreed with the flags on an answer, and have flagged it (as prompted) as "invalid flags" to indicate that I believe the existing flags should be ignored. On all of these that I've looked at that have been reviewed, I see "disputed - a moderator reviewed your flag, but found no evidence to support it", but the flagged content remains, which I assume means that the moderator agreed with my conclusion that the existing flags were not valid.
My naive assumption is that this is because when the existing flags are disagreed with by a moderator, my "invalid flags" flag is also pulled in along with the flags on the content, and is also considered "disputed", despite being commentary on the flags, and not the content.
This doesn't really bother me, but it seems to be a limitation of the implementation detail of "invalid flags", if my assumption is correct. Perhaps the way it is implemented should be changed so that a moderator agreeing with an "invalid flags" flag doesn't result in "disputed" in the flag history.