After the Downfall of Númenor, Aman was taken away from the world so that it could only be reached by the so-called Straight Road. It's unclear what this would have meant for the Enchanted Isles: all we can say for sure is that they no longer exist in the Bent World that came after this time. The natural assumption seems to be that they were removed from the world along with Aman, though it is not impossible that they were destroyed in the deluges that brought down Númenor.

It might be worthy of note that, during the Second Age, ships seem to have been able to pass to and fro across the Great Sea without obvious difficulty. We might take this to imply that the defensive islands of the West were no longer enchanted after the fall of Morgoth, and perhaps no longer existed at all. Given our rather limited understanding of the geography of the Enchanted Isles, however, it is hard to draw any definitive conclusions on this matter.

The geography shown here is based on a sketch map in volume IV of The History of Middle-earth. This is the most recent map we have showing the Enchanted Isles, but it nonetheless comes from early in the development of Arda within Tolkien's imagination. The arrangement of Middle-earth on this map is quite different from later developments, and similarly the Enchanted Isles may not ultimately have been intended to retain the configuration shown here.