Don't know if this has already been suggested, but an easy way to manage skipflags would be for each person to simply clear any skipflags they wish to use at the start of their segment, so there would be no need for "rationing" of skipflags. Now that I think about it, the same could work with regular flags, but you've already established a good system for rationing them, so it would be unwise to change it at this point.
edit: also, is there any specific way you want transitions between different modders' areas to look? It would look the most professional if the end of one area matched the beginning of the following area (i.e. end one area by walking off the right edge of the map, enter the next on the left edge of the map, or leave one area through a door, enter the next through a door). Is there going to be one standard way of doing this, or is andwhy just going to adjust the transitions appropriately so the area creators don't have to worry about it? Also, should we do something special if the player attempts to go "backwards" to the previous area, or just design the map so that's impossible?
edit: I'm guessing there should be a save/refill at the start of each area? Or just a save?