With two unrelated projects I don't see a huge problem... People are not going to confuse the two, and I dont want to go into which is "more appropriate". Both jsdb.org and jsdb.io are completely free to name themselves as they want. No trademarks, no infringements. It was honestly a really nicely appropriate and memorable name for the service.
It was also a steal for a four letter domain name :)
It was also a steal for a four letter domain name :)