@superpotato Actually, do to the way that update_post_meta works only fields that have new values are updated but WP still does a get query to check to see if it needs to be updated. This is the main issue. WP might actually be performing multiple queries for every field save.
@peterhintondesign I would probably have used a CPT for this rather than a repeater if I knew ahead of time that the rows would grow to this level.
There is no solution. The only real solution is to understand the problem and devise a solution that does not cause issues. For older sites that have this problem I have created a solution to the timeout issue, which is to detect potential timeouts, intercept them, let the save complete and and then send the user on his way after that. https://github.com/Hube2/acf-prevent-timeouts/
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