I don't know if someone had this problem before, despite i searched through internet i couldn't find anything related.
So basically when i package my level i can't see init.con, lowdetailtexture.dds, heightmapprimary.raw etc. It doesn't really affect level it manages to load up in-game.
I also tried in other levels, same problem occuring. Also tried to uninstall/install the editor but didn't help.