The only restriction the Flash upload has is a 2Gb max file size, and
that is due to the 32-bit architecture. Adobe says they are working on
a 64-bit version, but we'll have to wait for that.
In terms of file chunking, no, Flash is not capable of that. Java is
absolutely your best option.
If you are limited by your host then you should seriously look at
Amazon Web Services to host your applications. It provides you all
kinds of virtual computer "instances" that have no limits on them
except whatever the operating system foundation you choose has.
Anyway, I am dealing with similar issues, but only above the 2gb limit.
Oh, you could try using FTP, but Flash does not support FTP protocal.
Just saying in terms of other programs. FTP doesn't give you as many
options to capture data as HTTP, but it does get around file size