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Note that you might not necessarily be able to run any Groovy program on Hydro (Hydro program on Groovy) but assuming it does, you'd need to build it with your target installation sourced. To clarify, an example where your package is in the directory ~/catkin_workspace:

Every time you want to switch installations you'll need to do all of these:

source /opt/ros/groovy/setup.bash or source /opt/ros/hydro/setup.bash
cd ~/catkin_workspace
rm /devel -r
rm /build -r
catkin_make
source devel/setup.bash
rosrun my_package do_cool_stuff

Note that you need to remove /devel and /build (actually probably just /devel, but I'm not sure about that one) because it contains references to the current installation, ie it is Groovy or Hydro specific.