I seem to have lost much of my custom branding work after upgrading some WPMU-dev plug-ins

Hello!

I responded to the update WPMU-dev plugins prompt and when the update was complete I had lost most of my custom branding efforts. For example: help contents, favicon, custom log-in image. This is a real pain to redo, and who is to say that it won’t happen again with the the next upgrade. Please provide some assistance if possible.

Thank you.