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I had the same issue some time ago.
Headers (and Python files) generated by dynamic_reconfigure have their install rules auto-generated as well (see dynamic_reconfigure-macros.cmake, lines 52 and 53).
The name for the files is set some lines earlier (just the cpp line here):
set(_output_cpp ${CATKIN_DEVEL_PREFIX}/${CATKIN_PACKAGE_INCLUDE_DESTINATION}/${_cfgonly}Config.h)
If I remember correctly, I had an error in my .cfg file: the third parameter of the gen.generate(..) call did not match the filename of my .cfg. This led the CMake macro to generate a wrong filename (I had double ConfigConfig.h), causing the cannot find .. error upon installing.
You might want to make sure all the names you specified are consistent with actual and generated filenames.
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