If your data diverged at one site (old site receiving new content) and your code diverged on another (staging site in development) then you don’t really have a conflict here. You can just update live site with new code, assuming things are reasonably compatible.
In general WP is not friendly to bi–directional move of content. Usually workflows presume that content only ever moves in one direction (production to development, staging to production) and never in reverse. That saves one from a lot of trouble.
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