NCS3.1.1, Windows10, VScode, NRF52840 custom board
With 3.1.1 I've discovered the paths in the "Edit build configuration" wizard are being broken and silently ignored during the build.

The problem seems to be specific to the mcuboot paths, but I'm not 100% sure. The mcuboot paths are interpreted as relative to the NCS build path, instead of being relative to my firmware build path, and it silently ignores the "missing files".
If I use the nordic NRF connect "Edit sysbuild domains" dialog then I can specify the files, but not with complete paths. So I then need to use the "Edit build configurations" dialog to make sure the mcuboot paths are fully specified.
If I subsequently open the Edit configuration dialog and choose Generate, then it trims my paths and breaks them all again. And then silently ignores the missing files again.
In addition to this. I discovered that my temporary build files were going into a folder on c:\ncs\Iv2.6.0. And when I looked in my Output tab, I could see it was using v2.9.0 for various things. toolchains.json for example had the default set as 2.9. So I had to delete those toolchains and SDKs. from my disk and delete the build folders, remake everything with fully specified paths. and I'm still running into strange problems.
I've also noticed a "build" folder appearing sometimes, and I am not sure where it comes from. It suggests something isn't specifying the --build-dir folder sometimes so it's using the default "build" folder instead.
I've now created my own build commands that I run on the terminal because I am not able to work with the NRF connect sidebar reliably