Is there a way I can keep the page anchors associated with PDF links?

For example, A1 is converting:

mysite.com/test.pdf#page=2
to
./test.pdf

Toggling Cutout '#' seems to have no effect in 'Crawler options'

I believe the reason the setting you mention does not work is that the # is removed in the code that converts URLs to file paths. (And not during "scan" as such.)

I have forwarded it to support. (Please allow some time since it may require some analysis.)

If possible, email example website (or post URL here) to support email address at http://www.microsystools.com/home/contact.php