Scripting

Are you talking about removing inuse files?
Is this an legacy or MSI setup?
Files which was created by the application instead of the MSI package will not get removed and the RemoveFile table must be used in such case.

Here is some info I got on the PendingFileRenameOperations:
There are several applications, such as service packs and hotfixes, that must replace a
file that's in use and is unable to. Windows therefore provides the MoveFileEx API to
rename or delete a file and allows the caller to specify that they want the operation
to take place the next time the system boots, before the files are referenced.
Session Manager performs this task by reading the registered rename and delete
commands from the
HKLM\System\CurrentControlSet\Control\Session Manager\PendingFileRenameOperations
value.

Links regarding PendingFileRenameOperations:
MoveFileEx
PRB: Troubleshooting MoveFileEx() MOVEFILE_DELAY_UNTIL_REBOOT