First we don't support UNC for resource files. The next patch will restrict usage of UNC paths. Paths that are supported are either relative paths from the project directory or fully qualified urls e.g. http://localhost/site/resources/stuff.css
This is not however the sole reason for a loss of resources. We have a bug that will be fixed in the next patch.
I still lose files in my project, though not as bad as before. At the moment it's just one file at the end of the list. Details:
Also when upgrading the project to the latest SA release, I lost several controllers, views and models that I had to rebuild since SA has no import functionality. The odd thing about these lost elements was that the underlying files got a small first letter vs capital as it should have.
I'm reluctant to submit the whole project, but maybe an excerpt from the meta files could help?