You've uploaded 3500 files but your ftp client is only showing 1998 files in the folder. Why?
Our ftp server is configured to show only the first 2000 files in a folder. That includes '.', '..' and the first 1998 files. The idea behind the restriction is to stop rogue ftp clients continuously listing large folders and using up CPU time.
It would be better practice to split your files into multiple folders if possible. If that's not possible, please raise a support ticket to have the limit raised. We do not however recommend you allow anonymous FTP on folders containing that many files.