When you open a project with a missing toolchain (com.visualgdb.arm-eabi) it will prompt you to either retrieve the missing toolchain or use the current version installed.
This works as expected to update the toolchain of the first configuration. It does not however update the toolchain of other configurations of the same project.
I can open the vgdbcmake file and see that the first VisualGDBConfiguration in the file updates. All the other configurations use the old the dependency.
This would be fine if when you switch configurations it prompted you to update them, but instead it errors during cmake configuration and the only way to fix it is to manually edit the vgdbcmake file to update the dependencies.
System.Exception: Missing toolchain: com.visualgdb.arm-eabi. Please install it via VisualGDB Package Manager.
at u04.h4(IDELevelProjectInfoForBuilding a)
at u04.f3(lh3 a)
at u04.a2(k b, Int32 a)