Flattening script damages file

Question

I use Acrobat Pro 7.1.0 - Win XP SP2
I receive 2D monochrome CAD drawings from a vendor for approval. I add an "Approved" stamp and use the doc.FlattenPages() JavaScript command to make the stamp permanent. When I do this, some of the thin lines of the drawing become slightly modified/thinner and then only some of these lines will print properly. Others seem too thin to print.
Is there any way to modify the settings Acrobat uses during flattening to prevent losses or modifications of original data?
I have played a little bit with Hair-line repair but it doesn't seem to work for the circles, only straight lines. I would like to avoid making "touch-ups" as I have a lot of drawings to review.
I had this topic in the regular Acrobat forum, but it was suggested that this would also be a good place to post it.

Answer 1

okay. do this. open 3 files in two windows;
window a
file 1
file 2
window b
file 3
go to file 3 in window b and run the script
I was thinking the script would put all three files into one stack. It doesn't. It makes 3 copies of file 3 in a new stack.
It looks to me that it needs to be decided how this legacy script is going to accomodate windows.-probably by restricting the file selection to the current window most likely.