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You'll lose accuracy with anything other than proper type K extension wire. If the extension portion is all at the same temperature the error will be small or none. If the extension section traverses a temperature change your error will be greater. If you're just looking for relative temperature, i.e. you want to see if things are 10 degrees hotter at one time than another, the extension wire won't matter.
(I used to measure temperatures for a living)
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