Copying clips between Sequences in Premiere Pro CS6

Had to go back to Premiere CS6 because CC started crashing when viewing a clip in the Source window. Have to get work done so I went back to an older file in CS6. In CS6, I had two sequences I was working between and when I would copy clips from one to the other, I would lose audio on the sequence where the clips were going (video is viewble though). I could here it fine until I closed the project (after saving) and opened it later. The projects are identical, just one had a few tweaks to the edit. Same clips in the Bin. Any way of updating, relinking clips, fixing this issue?
Mac Pro
OSX 10.7.5

Seaspray - I will let the experts correct any bad advice here and perhaps I am adding nothing you already don't know or are doing. I recently went through the same exercise being new to PP CS6. Is that footage interlaced? I first drug a sample clip to the New Item button to create a matching sequence. I had some issues when I wasn't being careful about sequence settings matching, particularly putting interlaced in a progressive sequence. When I was ready to export, I chose the H.264 Blu-ray preset closest to my source footage. I made sure the key video characteristics matched - frame size, frame rate, progressive vs. interlaced, if the latter upper or lower, PAR, etc. etc. In some cases I tweaked VBR vs. CBR and bit rates. I then produced separate .m2v and .wav video/audio files. Then I imported those files as assets into Encore. You should then see Encore tell you it does not need to encode the video or audio after analysis. Unfortunatley, this process does require one encoding, but I don't believe there is anyway around that matter as PP CS6 apparently does not support "smart rendering". However, I think with just one encoding you are not going to see your footage noticeably degraded. Agreed, none of the monitors in PP or Encore should be used to judge quality. I also noticed major differences playing back files on my PC with various media players vs. PS3 + big TV.

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Copying clips between Sequences in Premiere Pro CS6

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