There is a known issue that replaces Class references with PLACEHOLDER or None which was fixed just recently. If you test a copy of your project in latest 4.7 from GitHub (4.7.4), does same issue occur? fix was implemented in this commit:
Could you upload your project somewhere and send me a link? I’d like to send this to devs if possible. If you need it to be private, you can send me link via PM on forums: