Remove Noise from Video Breaks Sync

I recently removed some audio noise from a video and the audio lost the sync with the video. Any ideas on what might cause this, and how to avoid it?
I have 8 files I need to clean up, and obviously not breaking them would be best.
Thanks!

Hi Wes,
Can you describe what happens a bit more? Is the audio late or early? By how much? Does it get worse over time? Does it appear out of sync within Soundbooth or only after you export it?
Thanks,
Durin

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