Unfortunately, it’s hard to suggest anything specific based on the description you provided. We could help you find the correct settings if you could let us know the following:
The .vgdbsettings (or .vgdbcmake) file with the transfer settings.
The exact path on the Windows machine where the file is located.
The exact paths on the Windows machine of files that et transferred despite being excluded.
It did get uploaded as expected (STM32 got excluded):
/tmp/xyz/2.cpp
/tmp/xyz/sub/3.txt
If you expect different behavior, please let us know the exact full paths of files on the Windows machine that get uploaded despite being excluded and the full path of the solution file.