In writing especially, not . . . because can give rise to serious ambiguities. Consider these sentences:
I didn’t go because I was ill. I didn’t go, because I was ill.
The problem seldom occurs in speaking. The first version, without a pause after go, suggests that I did go (to the doctor’s, for instance), but for some reason other than illness. The second reports that I did not go, and then gives the reason for my not going. The sentences would also probably be distinguished by a rising voice pitch in the first and a falling one in the second.
In writing, the distinction hinges – precariously – on a single comma. Many people leave out the comma in sentences with the second meaning. To be on the safe side, you could rewrite both versions. The first could be something along the lines of I went not because I was ill, but to get some jabs or It wasn’t because I was ill that I went. The second could become Because I was ill I didn’t go.
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