Pods has features when adding post types and taxonomies that are not available in ACF, for example post type relationships. Replacing these features could be problematic and/or require the addition of custom code that Pods uses to accomplish these features. This may be the reason that ACF has not include it on top of the fact that most people were using CPT-UI.
I would first make sure that I’m not using any special features that would need to be replace. That means only using the features available when using register_post_type() and register_taxonomy().
Then you would have to delete all of the post types and taxonomies from Pods and then recreate them with ACF. Deleting a post type or taxonomy in most plugins does not usually delete the posts or the terms associated with them.
All this being said, this is not something I would do, I don’t, as a general rule, retrofit client sites, they are what they are.
If I did decide this was necessary I would most definitely not attempt it without making a complete backup of the site before I started.
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