Right now projects cannot be merged (without a substantial amount of hacking). Mike has pointed out one of the problems, and a good workaround (two instances of the core application). Besides naming conflicts, there are many structural problems that should be solved before doing this. Keep in mind that a project recreates the state of the whole PixInsight platform, not just images. This is something that we'll have to implement eventually. Don't hold your breath, though, as we have tons of priorities competing at present.