According to The Digital Picture site, the 100-400L should be compatible with the Canon TCs, although no AF on the 6D. Still, it should work. I've used both my Kenko TCs at the same time with my 6D and 400 f5.6, so I see no reason for just one not to work with your 6D.
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Mark
markj.pics
"Life is uncertain, eat bacon now."
-UncleWede
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