Here’s what I just tried
1. disabled all plugins except ACF
2. changed theme to Twenty Seventeen
3. create new product
4. create new project
5. create new relationship field ‘test_field’ showing on product and project post types
6. linked new product to new project and published, relationship value is saved (on product edit page)
7. deselected the value and published; value not saved
I don’t think it’s a bug in the plugin but I tried everything, what else could it be?
