When you copy mixed long and short files names using Copy, Xcopy, and Windows NT Explorer, all files may not be present in the destination folder.
If a file with a LFN is copied and it generates a new SFN in the destination folder, it may be overwritten by an existing file in the source folder with the same name.
Q195144 explains the problem and shows an example.
The article explains that the "problem with Copy and Xcopy is by design" but a non-public fix for Windows NT Explorer is available from Microsoft Support (you must call).
You can also work around this feature by implementing tip 026, if your 16bit applications can open LFNs.