I need to copy data from one server to another however the only median we have is a small HDD. What is the best way to split up the data and merge it back on the other end without creating archives as the first server is full?
You haven't specified your operating system, which makes this question harder to answer.
However, HJSplit is a GUI file splitter/joiner available for Windows/Linux.
For the Linux/Unix command line, there's also
split, which can be rejoined with
cat. Usage instructions with an example are available on the Wikipedia page here.