Two posts, two different instances, two different sets of comments. Ok, there are pros and cons:

Segmenting the conversation means that different opinions and perspectives have a bigger opportunity to rise to the top in each discussion. That’s good.

There is also a risk of too few different viewpoints being present in one instance or another, making the possibility of an echo chamber forming higher. That’s bad.

I’m not suggesting that there’s a single perfect way to handle it, nothing is that black and white, but maybe there is a chance to do better. Perhaps crossposted content could contain a second link underneath between the body of the post and the comments section that could inform users that an identical post existed on another instance. Perhaps the comment sections could be merged but the user could choose to filter by instance if they wanted to.