Alexely, just making sure that I'm following you. You recommend that:
1) Align individual chunks
2) Align chunks (in my case they are aligned with common cameras)
3) Merge chunks (in my case everything is still a point cloud)
4) Optimize point cloud
5) Save project (Project A)
6) Save project under new name (Project B)
7) In "Project B", "Clone" the optimized point cloud from "Project A" by using File>Append and load. This will add a new chunk that has an identical point cloud (the one created in Step 3 from the merged chunks and optimized in Step 4).
8 ) In "Project B" place bounding box on small area of model in merged optimized chunk (from Steps 3 and 4).
9) Build Geometry, Build Texture, export to OBJ
10) Make active the "cloned" point cloud, Appended from Project A.
11) Place new bounding box adjacent to first bounding box area from Step 8 but in cloned point cloud.
12) Build Geometry, Build Texture, export to OBJ (being careful to use exactly the same setting from Step 9)
13) The two exported OBJs should fit together seamlessly in external program.
Specifically, you do NOT want to move the bounding box along the original point cloud, exporting several several OBJs from the same chunk. You want to build and export each chunk from a clone of the original point cloud. Did I get it right?
Thanks!
Mark