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I was able to build a mostly-complete .qch for OpenCV 3.1.0 as follows...

__Main Build__

cd PATH_TO/opencv-3.1.0
mkdir build; cd build
cmake -D CMAKE_INSTALL_PREFIX=/opt/opencv/3.1.0-qt5-gl \
      -D WITH_QT=5 \
      -D WITH_OPENGL=ON \
      -D WITH_OPENCL=OFF \
      -D BUILD_DOCS=ON \
      -D CMAKE_DOXYGEN_GENERATE_QHP=ON \
      -D CMAKE_BUILD_TYPE=RELEASE  ..
make -j7

__Documents Build__

cd doc  # goto PATH_TO/opencv-3.1.0/build/doc
make help
    The following are some of the valid targets for this Makefile:
   [...snip...]
    ... doxygen
    ... test
    ... package_source
    ... install/local

make -j7 doxygen

cd doc/doxygen/html
qhelpgenerator index.qhp -o opencv-3.1.0.qch

_NOTE: In my case, there was a unmatched, dangling </section> tag at line 37157. If needed, comment out this line and rerun qhelpgenerator._

I was able to build a mostly-complete .qch for OpenCV 3.1.0 as follows...

__Main Build__Main Build

cd PATH_TO/opencv-3.1.0
mkdir build; cd build
cmake -D CMAKE_INSTALL_PREFIX=/opt/opencv/3.1.0-qt5-gl \
      -D WITH_QT=5 \
      -D WITH_OPENGL=ON \
      -D WITH_OPENCL=OFF \
      -D BUILD_DOCS=ON \
      -D CMAKE_DOXYGEN_GENERATE_QHP=ON \
      -D CMAKE_BUILD_TYPE=RELEASE  ..
make -j7

__Documents Build__Documents Build

cd doc  # goto PATH_TO/opencv-3.1.0/build/doc
make help
    The following are some of the valid targets for this Makefile:
   [...snip...]
    ... doxygen
    ... test
    ... package_source
    ... install/local

make -j7 doxygen

cd doc/doxygen/html
qhelpgenerator index.qhp -o opencv-3.1.0.qch

_NOTE: NOTE: In my case, there was a unmatched, dangling </section> tag at line 37157. If needed, comment out this line and rerun qhelpgenerator._