I've seen a couple of times now where changing a subassembly configuration from "show" to "hide" cause the subassembly to disappear from a BOM.  Here's the conditions under which it happens.  I put an assembly on a border.  I create a BOM set to show parts only.  I notice some subassemblies I need to have in the "hide" condition.  I want to see the subassembly on the BOM, not the subassembly components.  I open the subassemblies, change all configurations to the hide condition, then save and close the subassembly.  Instead of the subassembly now appearing on the BOM, it is gone altogether.  If I reinsert the BOM, it shows up.  I'm currently using SW 2016 x64, SP 4.0.  I've never seen this happen prior to this version of SolidWorks.

Here are a few things that the two assemblies in which this occurred have in common:

1.  They were both done in outside design houses.

2.  They were both put into a zip file and sent through a web file sharing service

3.  The subassemblies that disappeared are models downloaded from vendors, mostly air cylinders, and translated into SolidWorks.  They weren't all from the same vendor, and they probably were all translated from .stp files, though I'm not positive about that.

I still had the zip file from one of the assemblies, and I was able to recreate the problem.  I've tried to create the problem in other assemblies, but I haven't had any luck yet.  Has anyone else seen this before?