You can get it in/out with the pipe in place, but it is unlikely to be easy due to the probability of the blanking plug having seized in the hole. You can't use a lot of brute force because the pipe isn't that securely attached to the bike and you're most likely to break something, plus there's not a lot of room for wielding a spanner! Best to remove the header and then you can clamp it in a vice and apply heat if necessary and you'll have plenty of room for spannering.

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