Site Customisations Disappeared After Using WPMU Dev

Hello,

I have just installed WPMU Dev and slightly disappointed at the fact that some CSS and theme customisations have completely disappeared. I have paid a considerable amount for developers to make these changes and it's a shame that the plugin has done this.

How can I fix this? Will I have to have these customisations redone?
Just to reiterate, the issue is mainly on mobile as the mobile header was custom made including a search box, logo and mobile toggle.

Thanks.