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For the devel space rosrun looks first to the source space because that allows you to modify your scripts in the source space and have those modifications take effect without rebuilding. This obviously only works for scripts written in interpreted languages. I imagine you install the conversion script using a CMake snippet like this:

install(FILE src/conversion DESTINATION ....)

This means it is only installed when you invoke the install target, i.e. catkin_make install, and nothing is done in the devel space, i.e. plain catkin_make.

It looks like your setup will work fine if you just make your source copy of the script executable:

chmod +x src/conversion