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You should be able to work with your projects in Ulysses core and Ulysses Standard simultaneously. And there should also be no data loss. Ulysses core just does not expose several features while it still loads the full project. However, we would not suggest to use them mixed if you rely on features of the full version - like bookmarks. This may bring up unwanted side effects...
You should be able to upgrade your old license to core as well. No problem from our side :)