Hmmm... I've been in that situation before, putty'ing in, and wishing I could stop a process. I'd say background it, then, when you get home, foreground the pup; that should work. Here's how:
In the window that you have the task running from, press:
CTRL + Z
This should/will background/pause the process. It should throw up something like "1234+ stopped" where 1234 is the PID IIRC. Then, close it all down, get home, log in as that user, and type:
To forground the process; bringing it back to the front, and starting right where it left off.
If this does not work, or if you meant something else, please post back!