I released a new uptade to support the new file format.
Download again.
This result is right because scale isn't the same as flip.
Go to Spine editor and set the root bone to -1, you'll get the same result.
Furthermore you are using the function wrong way. (it worked for purely coincidental)
You need to call it as "spine_bone_set_scale_x(skeleton_id,bone_id,sx)";
So the right way will be:
bone = spine_bone_get_id(skel,'root');
spine_bone_set_scale_x(skel,bone,-1);
//...
sy = spine_bone_get_scale_y(skel,bone);
rot = spine_bone_get_rotation(skel,bone);
name = spine_bone_get_name(skel,bone);
spine_bone_set_rotation(skel,bone,angle);
//...
To really flip use "spine_skeleton_set_flip_x(skel,flipX)" in the new version.