Not sure if you’re still looking or have figured something out, but just in case someone is trying to do something similar.
Without seeing the code or knowing the theme you’re talking about I would guess that this is because there are 2 different forms.
There are a couple of choices, and to be honest I don’t know if either of them will actually work.
The first is to find a way to add inputs into the theme form and then use the ACF update_field() function to save the fields when the form is submitted. The problem here is getting your new fields into an existing form.
The second would be to see if you can add the theme fields to an ACF field group. If the fields are stored in the postmeta table this could be done by duplicating the field names used by the theme, this would cause ACF to save the fields when the ACF form is submitted. The problem here is there may be some problem on the back end where these fields appear twice.
