I've made a Custom mesa with TerrainControl and use the ReplacedBlocks feature to replace stone to Hardened Clay and Sandstone to Red Sandstone (Sandstone gets generated automatically under Sand, but unfortunately it generates normal sandstone under red sand aswell). But as shown in this video, sometimes it has some visual glitches, so the client displays some chunks as if they weren't replaced. If you update the block, it gets displayed correctly. And if you select chunks and regenerate them with worldedit they don't get replaced at all.

Here is a video:
https://youtu.be/MYUVLH0I6zg

I'm pretty sure we've never accounted for worldedit //regen command before and we don't have control over how they do that process. If you could provide client/server version as well as server type that would be of great help when we get to this bug! Thanks :D

"This server is running CraftBukkit version git-Spigot-0359393-9a17f01 (MC: 1.8.8) (Implementing API version 1.8.8-R0.1-SNAPSHOT)" (Custom version by @Howaner though...)
WorldEdit 6.0 and TerrainControl 2.7.2
However, as shown in the video, the fake-untouched chunks are there without worldedits influence, but you can create real-untouched chunks with it.