The application cache is automatically checking and updating files every time the client visits the site. Lets say that the cache is only to be updated upon click of a button. The click adds the "manifest" to the tag, for only that request. At the next request, the "manifest" is removed.
Will the files still be in cache, or are they removed by the browser?
Will the manifest cached files still be used when the manifest is not defined in the tag?
The files will be still in cache! Problem here is: appcache files will get used all the time. The page in the cache still holds the manifest entry. So you first have to remove the entry on server side, then update the manifest content itself so the agent will update the page in appcache again, now without that manifest entry.
I know this is an old question, but it's surprising how little info there is on this matter.
In conjunction with Marvin's answer, you can exploit a little known feature of the manifest to clear the cache:
If any of the files mentioned in the CACHE section can't be retrieved, the entire cache will be disregarded.
So, after you update the manifest, all you need to do is have the file that uses it point to a nonexistent manifest file, and then everything should be dumped.
You can use a little PHP to make things cleaner:
<?php
$CACHE = false;
?><!DOCTYPE html>
<html manifest="<?php if(!$CACHE){echo "BREAK";} ?>manifest.php">
