A ferramenta de sincronização fundamental é o onipresente rsync unix, e você quer no windows. Ele pode encontrar os arquivos ausentes e copiá-los. Pode fazer muito mais do que isso, mas parece que isso irá satisfazer suas necessidades.
cwRsync é basicamente o rsync para Windows que vem com uma GUI do cliente para facilidade de uso: link
Rsync uses the Rsync algorithm which provides a very fast method for bringing remote files into sync. It does this by sending just the differences in the files across the link, without requiring that both sets of files are present at one of the ends of the link beforehand. At first glance this may seem impossible because the calculation of diffs between two files normally requires local access to both files.
DeltaCopy é uma alternativa, você pode achar a GUI menos intimidadora, talvez também de código aberto:
link
In general terms, DeltaCopy is an open source, fast incremental backup
program. Let's say you have to backup one file that is 500 MB every
night. A normal file copy would copy the entire file even if a few
bytes have changed. DeltaCopy, on the other hand, would only copy the
part of file that has actually been modified. This reduces the data
transfer to just a small fraction of 500 MB saving time and network
bandwidth.
In technical terms, DeltaCopy is a "Windows Friendly" wrapper around
the Rsync program, currently maintained by Wayne Davison. "rsync" is
primarily designed for Unix/Linux/BSD systems. Although ports are
available for Windows, they typically require downloading Cygwin
libraries and manual configuration.