Hey Heinrich,
You need to add all the files to wyBuild that constitute a version. See the Step-by-step walkthrough.
So, for your example, in the 1.1 version tab in wyBuild you'll have the following files:
text1.txt
For version 1.2, the following files:
text1.txttext2.txt
For version 1.3, the following files:
text1.txttext2.txttext3.txt
wyBuild does the hard work of actually detecting what has changed between versions and creating the tiny patches.
The way you have it set up now, wyBuild reads version "1.3" as saying delete all the old files from previous versions (i.e. "test1.txt" and "text2.txt" are deleted) and the new "text3.txt" is added. The reason is that in your version "1.3" you only have the "text3.txt" file instead of all your files.
Short answer: include all the files for every version. wyBuild detects the differences. If you do it the way I just described (and descibed in the walkthrough) then wyBuild will have the behavior you expect.
Does this make sense?