The timeouts actually have to do with the browser. >30 seconds and browsers will generally show a timeout message. This can be an issue with ACF when there are a lot of fields to be saved without adding any overhead for adding the content to post_content. This is purely a case of the number of queries involved because WP only updates one meta value at a time and each update can take 2 to 4 db queries to complete. The first time I saw this issue was on a site where each layout had up to 7 wysiwyg fields. This site would time out just saving ACF data (without the extra processing) at around 10 to 15 layouts (as many as 135 wysiwyg editors), depending on how much content was being saved.
Just a note that the timeout in this case will not cause the data to not be saved. Since there is no communication with the browser until php completes all the saving it completes before it knows that the browser has disconnected. When this happens you simply need to go back to the admin page and reload it to see all the changes. I supposed, it really extreme cases PHP could also timeout, depending on what your max execution time is, and that could cause an issue with the data actually being saved.
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