I was running Piefed, but switched it to Lemmy after a while, it’s done through the same domain. I am running a Fediverse server through a Cloudflare tunnel, had some major de-sync issues with Lemmy.world, and a new account seemingly resolved them. I am not sure if all is working well or not. My terminal is spamming me with inbox post requests to lemmy.world and I am unsure if this is normal or not.
Your instance would have private/public keys for communicating with other instances. By changing software, all that is gone, and you might find other instances rejecting your federation activities, this is doubly true if you used the same username, because they would already have a record of that user with a different public key.
I’d suggest using a subdomain or a new domain, re-using a domain for a different Fediverse server is likely to have issues. A subdomain would be treated as a different domain so would be fine.
This is also something to know for a different scenario: taking your lemmy instance and changing the domain but keeping the content is likely to break federation as well.
I’m gonna try and hold out and see what happens. Piefed did not last long, it did federate with quite a few servers, but I was mainly browsing content on my one account.