It's safe to remove a database from one project without it affecting the records of the database in another project.
Basically, when you remove a database (and choose to delete history) we delete object records for that database only when those records don't exist in other projects.
Typically it makes more sense to have a given database in only one project but we allow for it. You'll notice that if you check out an object in a project that same object will be checked out in any other projects that it may exist.
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