Put a "Declaration" field at the top of your file, setting it to "#ifdef MY_MACRO" and "in source file only". Do the same with "#endif" at the bottom. This should be enough to no generate any code from the FL files.
You can do the same again and set it to "in header file only" to also exclude whatever is in the header. Anything that is left outside (#include <FL/Fl.H>, maybe a few other lines) will not generate any actual code.
If you want to exclude even that, check the first line in your generated file. It should say something like "#ifndef my_file_h". So if you define the macro "my_file_h", the header will no longer be loaded.
But the best solution is probably the modify your Makefile/CMake/whatever file to not generate and compile the Fluid files in the first place.