This change is mostly affecting Pix4Dengine users that were using scripts to create the correct coordinate system directly in the .p4d file, but it applies to all versions of Pix4D software.
From version 4.0 to 4.1 of the software
- WKT strings of compound CS (defining both horizontal and vertical systems) were supported in 4.0. They are not supported in 4.1. This choice makes CS definitions more explicit and splits responsibilities more clearly: wkt defines the horizontal CS, verticalDef defines the vertical CS.
- In version 4.0 and prior, WKT strings of compound CS were not handled as expected. A compound CS defines a horizontal and a vertical part, however Pix4Dmapper would only extract the horizontal part and use the vertical CS defined by the verticalDef overriding the definition from WKT.
The details on how this works are described in this article from the Knowledge Base.
Feel free to ask questions in the comments.