Disconnected Use(with external drive)= Corrupted file structure

Help. Really like the way LR handles RAW. Big problem for me is that my Mac Book Pro HD is too full. I'm using an EHD from OWC(FW800). If I launch LR with the drive unmounted LR starts verifying files and pulling all sorts of garbage into the LR Folder panel. If I reconnect the drive there is no repair and only a fraction of the files show up with their terminal folder- the folder structure on the EHD is flattened to useless. Fatal flaw? or my error?
Thanks,
Steve

Hi Dan- Happy to try and help. It has happen under 2 scenarios, the lrdb files are at MacHD/users/srp/pictures/LightRoom/...irdb in both cases.
Scenario 1: I had a folder with some duplicates in MAC HD/users/...pictures/My Photos/duplicate files. When I would dismount the EHD and launch LR it would pull the dups on the Mac HD into the DB and reference what looked to be temps for missing files as well with fairly random preview distribution. The EHD file structure is OWC/users/srp/pictures/My Photos/files by date.
Scenario 2: I ditched the duplicate folders on the MAC HD (they were not referenced in LR before disconnect anyway) and launched LR. It initiates checking for files and photos again and pulled random preview references to odd files replacing the original folder structure. In this case there were no valid references to pull so it was mostly garbage, it did preserve a few "?" files.
Folders Panels: http://aktlr.smugmug.com/gallery/2668872#141260988.
Ive included scenario 1 & 2 grabs and an example of a garbage path
My work around is that I delete the lrdb and replace it with a clean copy, better than re-importing everything.

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Disconnected Use(with external drive)= Corrupted file structure

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