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I don't know for sure, but probably it is somewhere in ~/.sage There is a subdirectory there having to do with the notebook, and presumably the tab completion data is somewhere inside. Probably there's no great harm in deleting some of these files (unless you have important data in the notebook -- if so, save it elsewhere first!).

As an aside, this probably qualifies as a bug in the notebook interface to magma -- let us know if you have further difficulties, or other comments about how this should or shouldn't work.