env reporting environment variables starting with exclamation mark (possible path problems)?

To keep the long story short: I am generally a happy user of MINGW64 and MSYS2, and try to regularly keep updated. Eventually, I wanted to refresh a project I'm building using CMake - and suddenly, it started failing. It appeared to me that it is trying to build in some wrong directories, so I decided to check env - and I saw some variables I've never seen before:

$ env
ProgramFiles(x86)=C:\Program Files (x86)
!::=::\
CommonProgramFiles(x86)=C:\Program Files (x86)\Common Files
!C:=C:\Users\user\Desktop
...

I really don't understand how can a variable name be named !:: or !C: - the !C: one seems to be related to the folder where the MSYS2/MINGW64 was first started. I cannot even echo the content of these variables, and I cannot unset them; interestingly export -p does not report them.

I tried asking in https://stackoverflow.com/questions/76355596/env-reporting-environment-variables-starting-with-exclamation-mark-msys2-mingw6 but I doubt I'll get an answer there. In any case, I cannot recall ever seeing these "exclamation mark"-named environment variables ever, so I guess this is something recent. And the only reports I found, that I thought might be somewhat related, are:

• https://github.com/msys2/msys2-runtime/issues/152
• https://github.com/msys2/msys2-runtime/issues/150
• https://github.com/msys2/MSYS2-packages/issues/3605

Anyways - does anyone have any idea what do the !:: and !C: environment variables mean, and whether I could somehow unset them?

Btw, in my CMake project that is failing, if I call my "Windows" CMake install, like this:

$ /c/Program\ Files/CMake/bin/cmake.exe --version | head -n1
cmake version 3.14.3

$ /c/Program\ Files/CMake/bin/cmake.exe  ../ -DCMAKE_BUILD_TYPE=Debug -G "MSYS Makefiles"

... then most of my project builds, apart from one of the final targets (and it used to build fine in this setup a couple of months ago).

If I instead use the MINGW64 cmake:

$ cmake --version | head -n1
cmake version 3.26.4

$ cmake.exe  ../ -DCMAKE_BUILD_TYPE=Debug -G "MSYS Makefiles"

... then make fails almost immediately with the following (and it used to build fine also in this setup a couple of months ago):

/C/msys64/usr/bin/python3.11.exe: can't open file '/c/src/my_project/build/pico-sdk/src/rp2_common/boot_stage2/C:/src/rp2040_pico/pico-sdk/src/rp2_common/boot_stage2/pad_checksum': [Errno 2] No such file or directory

At least, I can tell that /C/msys64/.../C:/src/... is under no circumstance a valid path.

Is it possible, that these "exclamation-mark-named" environment variables !:: and !C: mess up path calculation as used the bash and/or CMake ...? Any ideas how do I get my build system working again?

Start by reviewing the linked msys2-runtime issues 152 and 150 and MSYS2-packages issue 3605, then reproduce the env output and the two CMake commands shown here. Trace how !:: and !C: are imported or handled and how that affects the reported /C/msys64/.../C:/... path. Done means the variables and path failure are explained, with a confirmed workaround or fix scope.