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If there's a message board, or some other situation where users are making frequent changes, and you want to make sure nothing is lost, you'll want to shut the site down during the migration.
Depending on the complexity and content of the site, there are different migration strategies. Also depends on where the new and old servers reside. If you are trying to transfer that much data over the internet, you will need to use a process that can be resumed.
I typically use rsync for such large migrations but it really depends on the underlying data, how it is structured in the directories and the goals of migration.
The tools built into Plesk/cPanel and their kin are designed for mass shared hosting. I find they fail once you start getting sites over 10-20GB.
Also, if you are running a single site. I would give up the control panel entirely and have someone manually configure the server for you. This reduces complexity, software maintenance requirements, removes control panel configuration issues and provides a more stable platform.
Once the big media is moved, delete it from the old server (or just move it out of the web root).
Now, use the built in site migration feature of cPanel, it should work fine now the site is small.
When it completes, copy the big media files into the correct folder on the new server. Migration complete.
According to various bits of info I found (including a discussion I found on the rsync mailing list) scp if often faster transfering compressed files (e.g. most media files) over fast connections (i.e. LANs). Rsync should be much faster transfering uncompressed files over the internet, or, AFAIK, when you have lots of small files only some of which have changed.
What the discussion on the rsync mailing list indicated was that sometimes you gain an advantage from rsync's ability to send only deltas etc. On a very fast network such as a LAN the overhead of doing that actually leads to worse performance, especially when dealing with compressed file formats.
This can even mean that copying an entire directory with scp can be faster than syncing it with rsync (for example if you have a directory of media files, most of which have changed). That surprised me.