How do I scale without loosing my animation? I have been trying to set the scale of this part from -1.000 to 1.000 but when I do that the faces flip inside out and the object completely looses it's rotation. 
Is there any way to do this, it is absolutely necessary for my project as it is for Flight Simulator and it does not read the scales as blender does and everything needs to be at 1.000.
I recommend using python. (mainly based on How to get keyframes and related information?)

for ob in bpy.context.scene.objects :
    if ob.type in ['MESH','ARMATURE'] and ob.animation_data:
        for fc in ob.animation_data.action.fcurves :
            for key in fc.keyframe_points :
                bpy.context.scene.frame_set(key.co[0])
                if ob.scale[0] &lt; 0:
                    ob.scale *= -1
                    ob.keyframe_insert(data_path = 'scale')


The flow of this code is something like;


look for an object
get the frame number with keyframes
rescale it if the scale is minus
overwrite keyframe


I've tried this with an animated .blend file in blender2.79 and it worked.