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Position the CTI (that blue upside-down triangle with the red line) at the beginning of the clip whose audio is missing. Make sure your track is active (ie. if Video 1 has the clip that needs audio, make sure its selector on the left of your timeline is lighter gray). Hit "M" on your keyboard; this will invoke the Match Frame command, which will open up the master clip related to the sequence clip in your source monitor. The CTI in the source monitor will be parked at the in-point of the instance of the clip; in fact, an in-point and out-point should already be set for the video portion of the clip. Right-click on the time bar and select Go to Clip Marker > Video In and then mark an Audio In, and then do the same for Video Out/Audio Out. Now your clip will have ins and outs for both video and audio, so simply edit over the unlinked video clip in the timeline. Don't use Replace Clip, as that will only replace video and won't add the audio.
And yes, you'll need to do this for every clip. Hopefully, you don't have many to do :) In the future, simply mute the track, or select just the audio portion of the clips and right-click on them and deselect "Enable". It'll save you lots of time... next time :D