Well, it turns out I was using an "old" Project Tool. Went over the documentation once more and downloaded the latest version. Ran it ... and custom settings (post build, source folders/filters, ...) all gone, again.
Fortunately, the debug options (location to cinema executable and g_alloc=Debug) remain as is. So, at list not everything gets cleared.
Apart from that I don't see what I am doing wrong, just launching the projecttoo.bat file containing:
Edit: going over the documentation again since months, I now see that removing "g_updateprojects", as mentioned in my previous post, would have been rather silly.