I made a simple pistol model, unwrapped it, baked maps (normal and ao) and exported it as .fbx to substance painter. In the material window of substance painter, the uv unwrap of the model looks like the first unwrap I did (which i changed because it wasn't good)
I followed "modeling weapons for a first person shooter" lesson for unwrapping and baking normals, and "texturing weapons for blender and substance" lesson for ao baking and exporting.
I tried unwrapping the whole model again, unwrapping and exporting only a part of it, copying a part of it to a new file and then exporting. None worked.
in blender check that you don't have that old uv saved in the mesh data. when you export blender will export that which in substance turns into overlapping uv:s from the two sets of uv:s.
Are you updating the model in Substance Painter when you make changes? When you export out the FBX it won't automatically update in Substance Painter as far as I know. You can go to Edit > Project Configuration then a new window will pop up. Select your FBX file again using the "Select" button. It will have your current FBX file, but in order to use the updated version you'll need to assign it again from here.
I had 2 uv maps under the data section. I deleted the old one and it worked. Thanks so much.
I made a simple pistol model, unwrapped it, baked
maps (normal and ao) and exported it as .fbx to substance painter. In the material window