Some examples of the resolution loss you are experiencing would help.
I can tell you that some time ago I did some exercises in transforming an image into some crazy shapes (spheres, waves, spiral) and found that upsampling previously the image in Photoshop to a size N times larger than the ouput size, allowed me to do these transformations using a hyper-basic nearest neighbour transformation (the only one my programming skills can afford), and still get a very high quality output.
Some examples here. As expected, straight nearest neighbour produced aliasing and information loss, but resampling the images prior to the basic transformation radically improved the result.left
: input image, centre
: straight nearest neigbour transform, right
: upsizing + nearest neighbour transform + downsizing.SPHERE MAPPINGWAVE MAPPINGSPIRAL MAPPING
Maybe if you previously upsize your scans, then apply the transform, and finally downsize to the final format can improve your results.