Hello
I discovered this also, after making lots of changes to the mesh and point cloud.
What I have since discovered, and it works every time, is to go to Tools, Preferences
uncheck the network processing option
make changes and then save the psx when done
when you want to do more processing such as dense cloud generation or mesh generation over the network, go to Tools, Preferences and check the network processing option.
When in network mode, some changes do not take effect like manual point deletion. Simply disable network processing while editing a psx file and Photscan will work like it is a psz file. Obviously, this should not be done while the file is being processed by other nodes.