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You should use a soft tonguing, like pronuncing the syllable "da", "du" (pronunced "do") or "di" (pronunced "dee"). The syllable "di" works better on the higher notes, because the tongue is closer to the teeth.
The most important part of tonguing is the air stream, and what you do with it.
For a piece like Bach that has many sixteenth note passages, you will want a constant stream of air going through the flute, and the tongue should only be interrupting that stream. A simple double tongue (Ta-ka-ta-ka or Du-gu-du-gu) should help you if single tonging is too difficult at the speed at which you take the piece. Just be aware of your air stream, keeping it steady and constant.
I know this sentence!!! and you must be careful to the harmonic phrase of the Partita, it is a writing polyphonic!!!
You know, I had a very good teacher!! ;-D
yes, I know!!! who is he?