Checked for Eclipse Luna 4.4.0 with Cdt 8.4.0.201406111759.
You may have a look to your workspace/.metadata/.plugins/org.eclipse.cdt.core/ and check for a file named like YourProjectName.language.settings.xml.
Delete this file (better should backup before), then reopen your project (or restart Eclipse) and Cdt should trigger the the GCC Builtin Discovery.
Note that this way may only applyable if your settings are set to project specific Builtin Discovery (not for »Use global provider shared between projects«). → see Project Properties → C/C++ General → Preprocessor Include Paths, Macros etc. → Providers → CDT GCC Built-in Compiler Settings.
For older Eclipse versions (IMHO about until Indigo), the scanner cache files were placed in workspace/.metadata/.plugins/org.eclipse.cdt.make.core/ and named like YourProjectName.sc.