Do you have any other clips in the Projects? So, what part of the clip are you deleting? Some part in the middle?
If so, then because of the magnetic timeline feature in iMovie 11, the clips will slide so the audio will then be out of sync with the video.
Question: What do want to achieve exactly? e.g. remove 5.0 seconds of video and replace it with 5.0 seconds of video from another clip or with a title?