Be aware that hunters this time of year will often be scouting out potential locations for a deer stand so that it can be set up now so the deer become accustomed to it before the hunting season begins. The flags could be the hunter's markers for his trail into the area he plans to hunt.
General advice for any flags out there is just to leave them alone and make every effort to follow the idea that cachers leave as little impact on an area as possible. If it is a hunter's trail or a survey trail, or some other legitimate use, you'll be in for the cache, out, and the person leaving the flags will never be disturbed. Same goes for nefarious flagging. Just don't mess with stuff, and you won't be messed with.
Of course, the hunter angle is a good reason to remind everyone that the time of year where international orange is MANDATORY is fast approaching. NEVER enter woods in the fall without it, whether or not it is hunting season. Not every hunter follows posted hunting seasons, and getting nailed by a poacher because you forgot your orange will definitely ruin your day.