Probably your already solved this (hopefully not by hand).
This part of your question is intriguing:
I found that if I open a post through WordPress front-end and then click “update” the custom field data and the post content “sync”
Do you mean back-end, right?
If so, I think a bulk update would solve this problem.
In wp-admin/edit.php
- increase the number of post shown (Screen options)
- select all
Bulk actions -> Edit- “change” some parameter, e.g. mark the same Author, o same Ping, or insert a temp tag you’ll delete later
Maybe, before increasing the number of posts shown, do a little test to see if it works.
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