This brings up 2 thoughts:
1.
Oncoman, this sounds like the way new trails are constructed. They do the middle first and do not expose the ends. When the trail is finally ready, they join the ends to existing trails, or a trailhead. Does it look like a good trail is being constructed, or is it just a series of flags, with no thought to proper trail construction?
Spencer, not that I know this is the case (a new trail), but unless you know for sure that it is NOT the case, it seems best to leave any flagging you find in place. Right now, there is a flagged trail up a mountain in the Catskills that could be mistaken for an 'illegal' trail, but it's a DEC approved work in progress. I would hate for someone to come along and remove all the flagging that was carefully added, after much planning and route finding.
2.
I don't know how much use this mountain gets, but if people are going to use a particular mountain a lot, there should be 1 well constructed, well maintained trail, rather than a bunch of bad herd paths all over the place.