In your project folder you will have .bundle directory that holds configuration for bundler. try deleting that folder. it should reset the install path for your gems back to system-wide settings.
In the case you just want to edit the install path, opening .bundle/config with your favorite editor should show you the path to vendor/bundle. Removing that line will restore it to defaults without removing other configs you might have.
Also, another less frequent scenario is your system-wide settings being messed up. According to @NaoiseGolden:
I had to delete
.bundlefrom my Home folder (rm -rf ~/.bundle). You can check out your configuration runningbundle env