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So the proper place to change this is in rosserial_arduino/src/ros.h. The numbers supplied there will overwrite the defaults in node_handle.h. I believe we split the template parameter BUFFER_SIZE into INPUT/OUTPUT_SIZE a while ago and probably forgot to update the docs -- be sure to change the template parameters for the chip you are actually using (note the various #ifdefs for different size AVR chips). Also, if increasing the buffer size, you should probably reduce the number of pubs/subs to keep down overall memory usage.

As for the chagnes not showing up -- perhaps it's not rebuilding due to the header file change? The arduino buildsystem is pretty funky, if you turn on verbose compile/upload under the Preferences menu, you should be able to see where it is putting the built files (typically somewhere under /tmp for linux machines) -- try deleting that folder to force a full rebuild?