Trying to understand the state of your sources to best advise. If I understand correctly, you have video with scratch audio VA and you want to remove the scratch audio and sync the double system audio to create a new sync clip? Or you want to resync the VA clip as it came in from camera?
I usually don’t sync in the timeline myself. If there are claps, (and assuming no common timecode?) I add a Mark IN at the clap on the VA clip, then a Mark IN at the same clap point on the double system audio. Select both clips and choose AutoSync from the Bin menu. In the dialog box, I select “use Mark In” as the sync method, then at the bottom I make sure “keep audio on video clip” is NOT selected and defaults as such. Select the range of tracks you want from the double system audio. Some like working with just the mix track if available or all tracks. Click OK. Your .sync clip in the bin will have removed the scratch audio from the original VA clip and added the double system audio.
I tend to always work in a 35mm 4 perf project even if not using film so that I can further sync the clip to a 1/4 frame refinement as I describe in my blog here: https://24p.com/wordpress/?p=16
Michael