Merging img that contain identical map-tiles is no problem.
Your GPS will only load map-tiles with different map-ID's, so identical map-tiles will be skipped.

If you are building your own custom maps be sure you use unique map-ID's because when loaded with other maps it's possible they won't be loaded. I experienced this with a map I created and it took me a long time to find out why it didn't show up on my GPS!