Subversion is a tool that keeps version history. This means that even if you delete a file, the historical representation of that file is stored.
The Subversion FAQ describes how to remove a file or a directory using svndumpfilter, which is also documented in more detail in The Subversion Book.
Using our dump file loader, you can reload a filtered dump as a smaller repository. If you run into storage issues while doing so, please click New Support Request to open a new ticket and we can assist.