Hello,
When publishing static files, it's a known issue that deleting an entry from MT does not remove the file from the file system.
Now I've observed the following:
I have categories in my blog. For example, travel. And when I publish, the category archive page is published as index.php and then each entry is published as travel/entry-file-name.php
Index.php contains the excerpts and links to the entries.
So I might have the following:
/home/user/www/travel/index.php
/home/user/www/travel/asia.php
/home/user/www/travel/north-america.php
I notice that when I delete asia.php and north-america.php then rebuild the entire blog, index.php does not get updated.
Notice, I DID NOT say that index.php does not get deleted. This is KNOWN behavior. But I would expect that MT would republish the category index as essentially empty (odd, but in keeping with the paradigm).
But instead, what I suspect happens is that MT's logic goes, "Hey there are no entries, thus I don't need to publish a category index." So nothing gets changed and the original index.php remains in place...
Specs:
MT 3.2