Ouch, owieee! A source control wrinkle!
I'm wondering if that's part of the issue. Are you working
with another author or a team? If so, were the folders and files
that keep performing the disappearing act created by other parties?
What I'm wondering here is if a project was updated by adding
files and folders by a member of a team, somehow Source Control is
causing the issue of making the content disappear on other
machines.
Cheers... Rick