Your problem may not be related to the plug-pulling at all.
Version 1.0 of Emplode/Empeg has a bug with V2 tags that contain long comment fields. Do your MP3 files fit that description?
If so, try deleting the 35 visible files, stripping the V2 tags off the files, and re-uploading them. What'll happen is that the Empeg will simply re-use those orphaned FIDs as you upload the new tunes and all will be well.
1.01 (coming soon) will fix this known bug with the V2 tag length.
Let us know if this fixes your problem.
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Tony Fabris