The file idea.properties, located in the bin directory of the IntelliJ IDEA installation folder, should not be edited. Instead of editing the original idea.properties, create file idea.properties in the location specified below, open it for editing and add the required properties.
So, depending on your platform:
What was that?
All IDEs based on IntelliJ platform have a global setting telling whether to treat file systems as case-sensitive. The setting depends on OS: by default, Mac OS X and Windows are case-insensitive, Linux and friends are case-sensitive.
Unfortunately, life is never that simple. The warning you've seen means that on opening a project an IDE has performed a quick check and found you guilty that case-sensitivity of a file system, on which the project is located, doesn't match aforementioned setting.
Is it bad?
Well, this won't set your computer on fire, but certain undesired things may happen - missing files, undetected external changes, file cache conflicts and excessive indexing among them.
How to deal
You can either move your projects, or tell an IDE to change its mind.
For the latter add the following line to idea.properties file (see this article for details):
Use true if your projects are located on case-sensitive FS, false otherwise. Then choose File | Invalidate Caches and restart the IDE.
Nope. Setting the global property is a temporary solution; vote/watch this issue to be notified when a permanent fix will be in place.