Pip stole some of it to give to the convict (after he was threatened by the convict to bring him a file and some "wittles", which is food) so he had to make it not seem like there was some brandy missing. He filled it with tar water.
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Uncle Pumblechook is unable to drink the brandy because he accidentally swallows a nutcracker while trying to take a sip, causing him to choke and gag. This humorous incident adds comedic relief to the novel and highlights Uncle Pumblechook's clumsy and awkward character.