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I want to get the absolute position of motor shaft, so I have added two magnets on the metallic thread (which holds the motor) and some hall sensors on top of shaft. Can the magnets in some way interfere with motor or damage it ?

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The magnetic field from your magnets falls of pretty rapidly with distance, and your motor likely has some magnetic shielding so it's very unlikely there would be any measurable effect on the operation of your motor from a couple of small permanent magnets located nearby.

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