IPFS> IPNS Even if I publish different folders, I always get the same peerID

Indeed.

It’s considered a bad practice to have multiple Kubo instances sharing the same PeerID/Key running simultaneously as it will create race conditions as described in this reply: How to import key to let others publish in same IPNS record - #2 by ylempereur

The main issue is that it “reprovides” the IPNS record every 4 hours. So, if you publish a new record on a node, it provides it. If you later publish to the same address from another node, it provides the new one. But, a bit later, the original node will “reprovide” its own record, walking it back. Then the other will reprovide its record, etc… The more nodes you have, the more they will fight (and only one has the real record at any one time). Also, they each keep the count locally, so multiple nodes will start providing records with the same count, but with different content. In the end, it’ll be a mess.

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