Can lightning destroy rails in Minecraft?

Solution 1:

There are a lot of reasons as to why parts might be missing:

1. Endermen
2. You could have taken some away without knowing
3. If anyone (say friends) has been on your server they might have taken them away
4. It could be the "SMP" glitch where you lay them then they disappear and come back into your inventory.

You might think these are silly reasons but these are the only ways they could have disappeared. =)

Solution 2:

Lightning can only destroy flammable blocks, and rails are not flammable.

This is more likely the cause of your problem:

since Endermen have (until recently) been able to pick up and move most blocks, including rails.

Solution 3:

I would also guess for endermen being the cause of your missing Rails. Until 1.8.x they were able to move most blocks of the game around.

So it is possible, that they take the block from under your rails and put it back, but the rails will drop. (this happened to me once)

From the 1.9 versions on, the endermen will only be able to take "light" blocks like sand or gravel, but not cobblestone, stone and other "heavy" materials. So it would save your rail if you place it on a cobblestone-path in versions 1.9-pre and up.

The full list of blocks an enderman can take in each version can be found on the minecraft-wiki: http://www.minecraftwiki.net/wiki/Enderman#Moving_blocks