So I ran into a strange problem today. I was having some issues with one of my modules in IntelliJ so I decided I should try blowing it out and rebuilding it from a fresh checkout. I deleted the module from the Project window and then deleted / redownloaded from my file system.
I went back to Intellij and tried importing the module. It took me through the normal steps of selecting options and then seemed to succeed. Only it didn't reappear in my projects window.
I'm not sure what I did, but recreating the whole project isn't an option at this point. I'm hoping someone can shine some light on why Intellij is angry with me.
System Specs: Mac OSX Mountain Lion IntelliJ 12.1.4
Ah ha! I think I found the answer.
In my .idea project folder there is a misc.xml. In this file I found
<option name="ignoredFiles">
<set>
<option value="$PROJECT_DIR$/../Projects/.../module/pom.xml />
</set>
</option>
I removed that and also cleaned up some duplicate entries from other areas that pertained to my module and I was able to import again.
IntelliJ is pacified for at least another day!