Well if the GSX freezes and nothing happens the only way to restart the whole process is by rebuild the cache.
No, only a normal Couatl restart is required. As I've said, rebuilding the cache is only required after adding/removing an airport IF GSX doesn't detect the change by itself.
When I say "somewhere during boarding it just stopped". means literally there. So I see the message bar updating all the time about the boarding process 67/119 and then nothing. The cargo is stopped in the middle, boarding also and when i hit ctrl+shift+f12 the menu is not showing up, even if I go the Addonss, GSX2, Show Menu, it doesn't show. No errors showing nothing.
No, it's not possible it would just stop, without showing any errors, because if it didn't respond to the Ctrl+Shift+F12, it's because there must been some kind of error.
So, be sure you have Logging enabled in the Troubleshooting page, and wait for that to happen. If it happens again, don't restart, don't do anything, and just exit the sim, and post your Couatl.LOG. If you restart Couatl ( with or without cache rebuild, which is NOT required ), the interesting log with the error would be lost.