if you're really set on using iframes (and I don't recommend it - they're a pain and accomplish nothing you can't do through php and css), I think it could work like this:
page.php
PHP Code:
<?php session_start(); // this line MUST be the first line on the page! NOTHING above it!
$_SESSION['user'] = $user; //set $user info from this page to be available to session, if not already done
?>
<a href="/path/to/popup.php">popup link</a>
popup.php
PHP Code:
<?php session_start(); //see comment above
?>
<iframe src="http://www.tosengine.com/NFDocuments/AS9100/<?php echo $_SESSION['user']; ?>/app.php"></iframe>
this could also be done through $_GET or $_POST, but I think $_SESSION would be best in this case, as user information is usually useful/needed across several pages anyway.
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