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If you are saving then importing, make sure you save with the opf file. That's an option on Save to Disk. The opf file contains all metadata and will reimport as it was exported if that file exists. If it does not exist, then make sure you have Add Books set to read metadata from the file, not the filename.
As to the issues where "The" is added at the end, (that will also happen with "A," etc.) that's happening for two reasons. First, you are using a library sorting order for your sort field and second you are saving to disk using the sort field. You can change either. If you change from library sort order, then it will not move "The" to the end of the sort field. Then you can use the sort field in your save template. Alternatively, you can keep "The" at the end of the sort field, and use the unsorted field in your save template.
I suspect you'll have more questions about that, but keep asking and someone will point you to the tweaks and save templates you will need for whatever you want to do.
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