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You won't be able to delete them if you've been working with the files. The thumbs.db is what allows you to view thumbs quickly so any image you've viewed is kinda open in that thumbs.db file. Turning off the thumb cache just means it will have to reload the thumbs each time you click the folder. A real pain if you are sorting content or designing a site. The only way you can delete all of these is to shut down your computer, restart it and OPEN NOTHING.
What are you using to ftp?
Leap ftp has a tick box option of which files to skip during upload as do most others ...
In leap ftp for example, go to options menu --> preferences --> general then select 'skip list' tab in the general preferences window. Tick the box 'enable skip list' and type 'thumbs.db' then press the add button.
Good luck!
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