One of the issues with Windows is the difficulty of figuring out whether a file is really open/locked. The Egnyte Desktop Sync application uses a rather strict test that opens a file with an exclusive lock, so any program that is accessing the file will cause a "file locked" message.
A good example is an anti-virus application that may be scanning some files while the Desktop Sync application is synchronizing.
To verify this, you may use a special Windows program to check if the file(s) are indeed locked. One recommendation is a program called Unlocker. You can download it here.
If a file is indeed locked by another application, the next synchronizations will typically pick up the file when it is no longer being used.