First try to deploy locally once and then commit. In most cases this is enough.
If the error remains you can use Tortoise SVN client (mind the correct version), connect with the repository and remove the files from the repository to solve this conflict.
When you browse to your local project directory, and right click the theme directory you should see a option Tortoise SVN > repo browser
Sign in with your Mendix ID and Password
Goto the folder Trunk > Theme there you can alter the contents in the repo browser on the teamserver.
But be very carefull using this option, you can delete the theme files by right click and choose delete.
I will try the tortoisesvn option, because locally deploying does not do the trick.