As suggested by Florian Straub to my comment, I added my comment as a response to the post, in addition to the comment on the original post.
We had a similar problem, although we used the WIX_IS_NETFRAMEWORK_46_OR_LATER_INSTALLED property. It turned out that we had WiX 3.9 installed on the build server, and 3.10 on the development machines. The upgrade to WiX 3.10 helped. Property doesn't seem to be allowed in previous versions
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