UV room is an extension of Paint Room, use it to tweak model’s UVs previously baked in Paint Room.
UV room and Retopo UVs are not connected on any way, they are total different meshes inside 3DCoat, one is called Retopo Object and the other is called Paint Object. 
Once something is in Paint room, the Paint Object cares only about what Paint, Tweak and UV rooms do.
So, to Update Paint room objects UVs, you use the UV room, once you hit the “Apply UV-set button” then it’s done, you don’t have to do anything else, you will paint, see and use the new UVs, even if you already have paint on it, 3DCoat will automatically re-project the paint layers to the new UVs, so it should look almost the same before you did any UV change.
Also, as a side note, If you need to or want to update the Paint Objects with the Retopo Object for whatever reason, like if you make a change on the topology and decided to create new UVs and all inside retopo room. 
You can use Bake menu and use “Update Paint mesh with Retopo mesh“, which replaces currently visible object in Paint room or “Retopo -> Per Pixel Object (no baking)” which doesn’t replace anything and creates a new Paint Object along with the ones you had before.
Sharp edges from Blender .obj export to 3DCoat
When export meshes as .obj files from Blender and then import them into 3DCoat for UV mapping / unwrapping all of the edges had been marked as sharp which made it harder to see the marked seams and messed up the baking result in the program.
There is a way to avoid this from happening in the Blender export .obj options. All you have to do is untick the “normals” option under the Geometry settings.
There are also options to clear sharp seams in the Retopology room in 3DCoat if you are in select mode for edges but it is easier and faster to avoid the problem in the first place.
Importing into Second Life
If you are bringing your mesh from other 3D software and changing the UVs, then you have to make sure you are importing into Second Life the mesh with new UVs you export using Export Objects and Textures (for Second Life, don’t forget to check Z-up coordinate system so it will be oriented correctly when you import it).
Tutorials
How to swap UVs: This video covers one easy method in 3DCoat, to modify a model’s UV’s after doing some texture painting work….without any penalty.
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