Hi,
I know this has been posted before for earlier versions, but the solutions suggested did not work. I've isolated the problem somewhat, and found a workaround, so I'm sharing it here, and hopefully it can be fixed in an upcoming version.
Version: Agisoft PhotoScan 1.4.3 (Linux and Windows both have this issue)
Problem description:
1. Delete some undesirable points from the dense point cloud.
2. I've tried both "Compact point cloud" and tried it without that option, the results are identical.
3. Choose "Workflow -> Build Mesh". Surface type Arbitrary, Reuse depth maps unchecked.
4. The resultant mesh has polygons for the entire dense point cloud, including for the deleted points.
5. To verify this, I tried deleting fully 1/2 of the dense points in the scene, and the resultant mesh still had the entire area including deleted points. I also tried deleting the sparse points, in case they were also being used for some reason, That still did not work. I tried this in linux and windows versions of photoscan and the problem exists in both. I also tried saving the project as a new file, and that did not work.
What worked:
Instead of using "Workflow -> Build Mesh" I used "Workflow -> Batch Process -> Build Mesh". I set the source type to arbitrary again, and Source Data to Dense Cloud. The resultant mesh did NOT include the deleted dense points.
This leads me to believe that "Workflow -> Build Mesh" is not using the edited Dense Cloud, but rather it is using the full dense cloud. By contrast, the batch process version does seem to use the edited dense cloud.
I hope this helps others, and I hope this gets resolved.