I’m guessing you have a lot of layouts with a lot of fields and it’s causing the db queries to time out the sync.
you cannot remove that filter, acf uses that filter for specific types of fields, including flex fields.
My question would be why are you syncing the field groups? I am assuming here that you have a site that you edit on (staging) and a live site. If this is the case, and you never edit the field groups on the live site and only sync them then there is no reason to sync them from the json files on the live site. In fact, these fields should only exist in the acf-json folder in the theme and not in the database.
If you do edit them on the live site then you’re going to need to find a way to reduce the number of fields in the field group. I would do this by using clone fields. I would create an empty field group for each layout and then I would “MOVE” the fields from each layout into it’s own group and finally I would clone that group back into the layout.
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