Yes, I expected that the future re-walling feature would fill in the mountain again, not just a fence. In my imagining of the Dwarf Fortress universe, Dwarves ought to be able to rebuild a section of wall or even close off a hallway without the option becoming a "game breaker".
Re-building a wall should be a serious time and material investment. I don't think you want a Legendary Mason to be able to build walls faster than 'Novice Mining' invaders could dig/destroy them! I don't know how many days duration, but maybe the raw material requirements would be 3-5 stone blocks per 'space'.
As for the issue of a re-built wall creating pathfinding errors: I do that all the time when I link doors to levers and I forget to "Pull the Lever" to open the doors. (Why can't my farmers find Plump Helmet Spawn? I've got 143 right here behind this, um, mechanized door. Oops!) So rebuilding a part of the mountain shouldn't(?) create any new types of pathfinding errors that players can't already cause through mechanisms or floods or cave-ins, etc.
The only other possible game-breaking issues I can think of might involve players who reach the chasm, but aren't ready for the creatures who are spawned by that trigger. So they wall off that hallway to prevent chasm critters from reaching them. But how is that different than pulling up a bridge or adding a flood or channel to block entrance for enemies? A re-wall would cause the same path-finding frustration to the antmen as any other defensive measures, wouldn't it?
And dwarves probably wouldn't just build an ugly clump of stone, they'd build a beautifully mason'd wall. So I'd expect it to show up as a 'smooth wall'. So purists would feel that they had to smooth all the surrounding walls (and floors?) to make it match.
How might you internally account for the re-wall "building"? I'd think you would have the dwarves uild it, but upon completion, it would become a mine feature, just like a smooth wall. It would have no built value, unless a regular smooth wall adds fortress value. (I doubt you could easily adapt your code to allow you to have a [d]esignation require raw materials)But my imagining of this feature would depend on the addition of mining creatures being able to dig. Which, aside from the federal limit of the 168-hour work week, is probably the real dependency for you to implement the re-wall feature.