Hi, Custom Edit mode should keep the last distribution of Generate mode without changes.
The only feature which would hide items both in Generate and Custom Edit mode is Camera->Limit to visibility.
Please, check if this option is enabled. If so, try increasing Expand and Back offset parameters, or directly turn it off. Anyway, it's not necessary to render, you can check the Clipping effect on viewport.
If Camera clipping is not the problem, please send us a simplificated scene to email@example.com and we'll check it.