I do something similar in reverse on one site using code like this:
[PHP]RewriteRule ^(.*)/(.*)/(.*) index.php?p=$1&r=$2&n=$3[/PHP]
…in htaccess
So someone linking to htp://www.mysite.com/a/b/c/ would be fine but it will actually call index.php?p=a&r=b&n=c (in this example) which means you can retain your credit. But of course, ppl will need to be told to link to /a/b/c
If you want to use the existing links you could reverse engineer that however you will have to know how to transform the directory /a/b/c to log their referer ID