Perhaps a screenshot showing us which 'faces' (other than shy residents) are disappearing?
For example are they related to certain stories? Do both the number and heights of your stories in all files match?
If they don't match in height, some elements may be there but hidden behind something. You can check this in the 3D window setting it to wireframe.
If a story is missing, add it to the file and then the missing 'faces' will appear as if by magic. Seriously though, the information is in the module, but can't show until the story is resides on is visible in the file.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"