Use merge project option
you need to choose piece by piece what you want compared or merged. it is not a one button solution.
My method when only changing program and data files is: using beyond compare for copying all the changes into the actual project.
I also had issues like yours in the past, since then I didn't try it again with the merge function. My method works for me, the methods and success in WoV change every now and then, I'm not willing to be the beta tester for Kuka.
I'm not sure if the WoV merge function works for sections of individual files.
So You can compare two projects, and insert the full config.dat from one at another, but You can't merge specific sections, as You would do using something as WinMerge, Beyond Compare or KDiff3.
As you want to give beyondcompare a try, check WinMerge too, there are plenty of file,folder comparing programs, this one is free and powerful.
Hope this helps.
