lucy24 - 9:23 pm on Apr 9, 2012 (gmt 0)
"Two versions of the header" is the first thing that comes to mind. Do your index and no-index files have something in common, like location, or are they randomly mixed all over the place? Are the headers constructed by a php script? (You said "example.php" but this is the HTML forum, so I can't tell :()
If the files are distinguished in some obvious way, it should be pretty trivial to write a couple of extra lines of php telling it to look at the name of the requesting file. If the name includes /openfolder/ use the OK-to-index version. If the name includes /closedfolder/ use the noindex version.
If the whole header is assembled on the fly, then of course you wouldn't need the different versions. You'd just have that one extra <meta blahblah noindex> tag, either included or omitted.