There's no harm in the roots being outside the pot, other than that as you said, it is easy to damage them when they stick out like that. If the medium it is growing in is old, then the roots will be reluctant to grow down into it, and therefore stay outside of the pot, but also roots sometimes just like to grow in the open air. Do you know how long it has been since the last repot? If it has been a while, I would repot into fresh medium, which will make new roots want to grow down into the pot, but as far as the ones which are outside the pot now, I would just leave them outside and let them do what they do. Trying to force them into a pot will probably break them, and since they are acclimated to growing in the open air, even if you could get them into a pot, they would likely die since they are not used to being buried.
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