Transfer the texture between two different sets of uv

Are the two sets well correlated? This would boil down to having a good set of vertex attributes for each set of uv's. If each set of uv's in mapping 1 has a know set of mappings in set 2 then it should be relatively straight forward to read from the first set of uv's and write to the second set.

If this is as simple as vertex 1 has a mapping in uv set 1 and a different mapping for uv set 2 then read from set one then resample the texture for set 2.

On the other hand if the two sets are completely uncorrelated then it gets more complex: A fully generic brute force solution would be to read 1 of the vertex attributes of the known mapping. Then search the entire set of uv's for set 2 filtering out those vertex positions that overlap with the current uv under consideration. Then use that list to read, resample and write the new texture.

The first case is easier to implement on the gpu. The second case is more difficult and may be better to implement on the cpu for debugging then move to the gpu as performance requirements dictate.

Edit for the first case: This is the easy case, Use the uv coords from set 1 on the gpu just like you would normally to read the texture. Then use the second set as actual vertex positions adding a z value that is some constant. Don't use a MVP matrix just go straight to clip space. The gpu will worry about the resampling. In the end you will have a fullscreen quad with the final mappings. Then just read the image back from the gpu.

More detail:

The vertex attributes for this would be:

Vertex Position = vec2{u_set2, v_set2}
uv coords = vec2{u_set1, v_set1}

The vertex shader:

vec2 remapping = vertex_position * 2.0 - 1.0; // remap x,y to -1 to 1
gl_position = vec4( remapping, 0.5, 1 ); 
out texcoord = uv_coords_in;

The fragment shader:

gl_color = texture( image_sampler, tex_coords);