Recapturing and replacing edited clips with incorrect aspect ratio

My camera settings were wrong when I captured the video. I edited the clips and discovered my mistake later. I changed the settings and my video looks correct now. The timecode runs perfect on the tape without a break in time. I tried renaming the clip after recapture but the scenes did not match up right. How can I match the timecode during capture. Hope this makes sense.

My sony hdr-hc1 outputs video with black bars when I record in HD but capture with a 4:3 setting in the TV type setting within the menu. I had changed the setting to SD 4:3 for a different project and forgot to change it back to 16:9 when I captured and edited it. I couldn't find out what was wrong until later. I changed the TV type to 16:9 and it fills the screen now. Even though I recorded in HD which is native 16:9 the TV type setting must match. I think it's pretty crazy myself. Any help on changing the clip out would be great.

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