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I'm not completely familiar with eclipse, but I presume that it uses the build rules defined in the CMakeLists.txt or that cmake generates the eclipse project, based on the CMakeLists.txt.

Either way, your CMakeLists.txt is missing the command which links your program against the ROS libraries. As described in the C++ publisher tutorial, section 1.3 and elsewhere, you need to add a target_link_libraries() to your CMakeLists.txt, like:

target_link_libraries(vel_cmd_filter_node ${catkin_LIBRARIES})

I'm not sure why it was working before; perhaps that line was there and you accidentally deleted it from the end of the file?