Nick, I've had very little sucess with FAS so this is untested advice. When you've opened the files you can reference them by name:
open blah
set docRefA to the name of document 1
open blah
set docRefB to the name of document 2
replace pages document docRefA over 1 from document docRefB starting with 1 number of pages 25
create thumbs docRefA
save docRefA to file (thepath & "saved_pdf:" & docRefB) as string) with linearize
I think your problem is "to alias" an alias is reference to existing file but you are making a new file that does not already exist. I hope I have that right?