My Canon 5000F has been a bloody nuisance ever since I bought it and I would advise everyone to have nothing to do with it. It works for a while and out of the blue develops an obsession, saying repeatedly that "maybe the scanner is not connected" - when it is - and says non-understandable things about its Twain thing. Once you pay money to buy something you expect it to work well, and this damn thing will not.
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Have you tried reinstalling the software? Have you tried a different USB port and cable?