So tell me why do I have to add all files from 1.1 just to make this small update.
Because wyBuild compares the versions and generates the smallest possible patch file. Thus you need to add all of your files that consist of the version.
If you only add some file then wyBuild will see "hey, that file existed in the old version and doesn't exist in the new version, therefore the user wants me to delete that file".
I have to upload 1.2gb everytime I make a small update?
File->Properties->Update & server files, uncheck "Create a catch-all update...".
and users have to download 1.2gb again ?.
No, they download a small patch file.