InFin,
When you refer to the fact that your machine will not boot I assume you mean it will not successfully load windows after you have copied all the files, it just goes to C:> prompt or close to this.
If this is the case then try this.
1) Format the desired HD (Large one)
2) Use Sys to create a bootable HD. By this I mean that a C:> will appear when you turn the machine on.
3) Copy all the files off the source disk (Small one), to the target disk (Large one) and tell it to replace any files it asks you about. If you reboot you should be able to start the machine and be in Windows. A few drivers may reload as Windows readjusts to the new HD but all should be fine.
The reason for this is that Windows makes some minor changes MSDOS.SYS and IO.SYS. If these files are from a different copy of Windows then the software just freeks out and goes off into the weeds.
If this fails contact Velvet and she will be able to get me and I can think of something else.
Have fun......