Recapture problem - Duplicate Item Filename

I forgot to choose Stereo Pair when capturing my clips in a project. FCP wont send audio clips to "Soundtrack Pro audio file project" if the clip is not captured as a Stereo Pair. If you try making an audio clip Stereo Pair in your sequence, it still wont work. Soundtrack Pro requires that your clip is captured as a Stereo Pair. I want to recapture my clips, but that is for some reason easier said than done.
I ctrl-clicked the clips in my browser, chose Make Offline, and then chose Move to trash. When I choose "Batch Capture" on my offline clips now, I get a window that says "Duplicate Item Filename". It says "A file in use by Final Cut has been found to use the specified filename. Enter a different filename and click Continue or choose one of the options listed below." The options that it lists are greyed out.
I found this problem as an archived thread here in the FCP forums, but the information there did not really help.
Should I just have removed the clips inside the Capture Scratch folder, instead of using the Make Offline feature?
I have emptied the trash, tried rebooting my Mac, repairing permissions, trashing my preferences. Nothing has helped. I am now trying to erase the free space on my media drive (which is as good as empty now).
Where is this filename information stored? Why does my FCP project think the offline clips still are on my media drive?
Please help

Thanks Andy.
I have done some more testing now. I made a backup of my project file, before I tried the "Make Offline" feature, and I also have backups of the project file inside my autosave vault.
When opening my project backup file, I get the usual message about offline clips and reconnecting. Batch Capture works great when clips are "missing". I get no message about duplicating item filename or anything like that.
The problem now, is that if I want to modify the clip settings of the missing/offline clips (and make them Stereo Pair), I can't because the clips are not offline but missing. If I check the source column in the browser, I can see it still thinks the clips are supposed to be on my media drive. To be able to modify clip settings, I have to make the clip offline. Once I do that, modifyinig the clip settings works, but when I try to batch capture a clip, I get the message about duplicating the item filename again.
Man... this bugs me.
UPDATE:
Wow.... I think I found the problem. Batch Capturing after making the clips offline works fine. This "duplicate item filename" message only appears AFTER I have modified the clip settings, making it Stereo Pair instead of dual mono. How annoying! This was my main goal. Recapturing the clips with Stereo Pair audio

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I have a number of offline items I am eager to digitize. When I select any of them or all of them and select Batch Capture then press OK in the Batch Capture window I get a window that states "Duplicate Item Filename". It says "A file in use by Final Cut has been found to use the specified filename. Enter a different filename and click Continue or choose one of the options listed below." The options that it lists is greyed out. These filenames it thinks it is using are not on my system. I have searched and searched and found nothing. But if I can't batch capture I can't use FCP. Too many clips already logged. Has anyone experienced this same problem and if so what did you do about it?

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Recapture problem - Duplicate Item Filename

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