It is my understanding that there are currently 3 arbitrary limits on which files will sync:
Only the first 5000 items in a folder will sync.
Only files smaller then 5 GB will sync.
Only 600 subdirectories will sync.
Limits 1 and 2 are currently causing significant problems for our company and I'm sure that it is only a matter of time before 3 becomes a problem as well. We would like to store more of our data on Egnyte backed local servers but these limits are making it difficult to do that and, if not addressed, may ultimately force us to look for another service.
Limit 1 is a problem because some of the software we use creates automanaged project directories that may contain tens of thousands of files. Because these directories are automanaged we can't restructure them into subfolders without breaking the associated project. Number 2 is a problem as we are a media company and routinely work with files and archives larger then 5 GB.
These limits are not intrinsic to any modern filesystem or transport protocol, that I am aware, of so I would like to see them removed. I know that Egnyte has been working on their backend infrastructure and I was told by support that the 5000 file limit is on the development roadmap for May 2012 so I'm hopeful that these issues will be addressed. Hopefully, other users who are, or expect to be, impacted by these limits will comment on this issue as well.