Windows 2003 Server with SP2
When attempting to upload a modified template you get the error message that says that access is denied to a shortcut file (*.url)
Access to the path C:\Program Files\PROJECT in a box Professional\Template2.0\ <template folder name>\<filename>.URL is denied (piabdb.clsDb.TemplateAddTemplateFiletoDoc)
This is caused by a problem with Windows 2003 reported in this KB article
If you look at the properties of file above you will notice that it no longer has a security tab.
Refer to the KB artcle above. You will need to delete the specific template folder and contents (to remove the offending .URL file) NB do not delete the the template2.0 folder. You will likely need to reboot the server before deleting the 'url' file.
You could also create a new ACL for the file in question using CACLS. From a command prompt go to the folder containing the .url file and run
cacls "<file.url>" /t /e /g administrator:f system:f
This should create a new ACL list for that file giving 'administrator' and 'system' full access. You should now be able to delete the .url file.