@Rellwood:
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1) Is there a way of totally protecting a bit of metadata once set? I really want to protect some parts of my metadata once added. Dates added, read, book source, etc. Since these shouldn't change once entered it would be really nice if I could just add it one time and then set the column to protected. Also, is there a way to lock in that metadata to survive a book merge, or transfer to new library
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For Standard Columns, it depends on the column.
If you were to create a Custom Column as a proxy for a Standard Column such as "modified date", then that proxy Custom Column would not be changed unless you changed it.
Book merges are more complex, and you control the settings for those in Calibre > Preferences. You should read the Calibre User Guide about this function, and also search the "Library Management" subforum about this.
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I am not sure if this is a part of the "Embed metadata" function
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Embed Metadata is all about embedding the book's metadata into the physical book file itself. You can read the Calibre User Guide about this function, and search the "Library Management" subforum about this.
DaltonST