winscp synchronize command fails on removal of remote files because IIS has file locked.

I have been successful with winscp and the synchronize command to remote server. Unfortunately once IIS has started it holds onto dll's and will not let winscp delete them. How can I efficiently remove files in remote directory before putting new files in remote directory?

I have tried other options such as the 'call' command to execute a bat or exe file on remote server, but that too has been unsuccessful.

Any help would be greatly appreciated.

Sorry, this is quite broad and unclear question.
So it's Windows server, right?
In general, if the file is locked you cannot delete it. Definitely not via protocols like FTP or SFTP (you didn't specify which one are you using).
What DLLs are those?