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One possible method:
Create a new calibre library. Call it "in". This is a repository for all books, unchanged.
Add all books from the two trees to "in".
Handle duplicates and bad books. Delete obvious junk.
Create a new library. Call it "finished". (Or "fiction", "non-fiction" and so on if needed.)
Copy a few books to "finished" from "in". 5-10?
Keep the books in "in" but tag them as "added to finished". Makes it easier to avoid duplicates in "finished" in the future. And you have a backup is something goes wrong.
Fix ALL the books you just added to "finished". Perfect metadata and cover and so on.
If something remains fixing, move the book back to "in" and tag it "todo". Or possibly use a small "working" library.
Setup a system to backup your calibre libraries.
When you download new books, add them to the "in" repository and handle them when you have time. Perhaps one author at a time or a series at a time or when you need something to read.
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