After adding a new drive to my machine and re-installing Windows, the path of my custom-built Qt directory changed from D:\Qt\4.8.3 to E:\Qt\4.8.3. CMake cannot use it in the new location, because it calls qmake -query which returns the old paths which are hard-coded into the Qt binaries.
The solution is simple: create a qt.conf file in the same directory as the qmake binary containing:
[Paths] Prefix = E:/Qt/4.8.3
The corresponding Qt documentation page has more details.
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