Search sync is one way from UR to the file system. You're wanting the opposite -- from file system to UR. You would need to use folder synchronization for that, which is currently two-way.
Regarding your question about preventing a second item from getting created with folder synchronization, if you create an item in UR within a synced folder, you would need to add a URL item attribute to that item, with a value of the folder + filename of the synced file.
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