This is the uber disappointing response that I got. I had to move to a different plugin. Can’t sell a theme that runs that slow:
This is a known issue with large amounts of ACF fields, and as you pointed out, with conditional logic.
Some people have managed to reduce the load times by the following methods:
Increasing max_vars as seen here: http://www.advancedcustomfields.com/faq/limit-number-fields/
(The link is about people not being able to save extra fields, but increasing max_vars and memory available to PHP should still increase performance with your issue.)
Installing a plugin that limits the number of revisions wordpress saves.
I’m sorry to say that these will both only increase performance slightly, if at all.
There is not really a way for ACF to “fix” this in the future, as ACF is just an easier way to access wordpress’ built in custom post functionality.
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