Hello Tomasz,
quite a bit of information you gave us here =)
I suggest you should check whether you have activated "Build Automatically" in the Project Menu of the Designer.
Also you could check your Designer preferences, in the XPages menu, check the Automatic Recompile option.
Other tips I can only gave you with some additional information. What are you doing? Which changes should be applied? Are we talking about Java, XPages, ScriptLibraries?
Hope this helps..