Can we directly make changes for ApplicationConfigurations, while game is running? For example, I have SettingsScreen, and when I press some button for changing to full screen, it will take effect instantly.
Yes, you can.
To change to fullscreen og change window size while game is running:
Gdx.graphics.setDisplayMode(int width, int height, boolean fullscreen)
[EDIT]
sry, I remembered this from an old version.
It is now:
Gdx.graphics.setWindowedMode(int x, int y)
and
Gdx.graphics.setFullscreenMode(Gdx.graphics.getDisplayMode())