cmake system fails to update config.h

## Description

When .config is tweaked, sometimes cmake system doesn't update the `include/nuttx/config.h`.

## Reproducing

To reproduce, try following steps:

- Find an out-of-tree build folder, do `cmake ~/Projects/Nuttx/nuttx -G Ninja -DBOARD_CONFIG=rv-virt/nsh`
- Run `ninja` to build nuttx
- Use `qemu-system-riscv32 -M virt -nographic -bios nuttx` to check it (e.g. run `free` or `hello` from NSHJ) then quit.

The repeat the following steps a few times:

- Run `kconfig-tweak -e DEBUG_SCHED_INFO`
- Run `ninja` to see `Re-running CMake...` followed by more build logs.
- Run `kconfig-tweak -d DEBUG_SCHED_INFO`
- Run `ninja` to see `Re-runing CMake...` followed by more build logs.

We expect to see `Re-running CMake...` each time after `.config` is tweaked, however this isn't true if we repeat the above tweaking operations more times.

Currently I have to clean current folder and redo `cmake` command, and do `kconfig-tweak` before using `ninja`. This is tedious.