I have a custom boot media with an expired (self signed) certificate. I also made several modifications to the boot.wim of my boot media to do "my own stuff" prior to starting the sccm task sequences. Since my certificate expired, I generated a new boot media with new self signed certificate. Now I could (and should) alter this new media with all modifications I made to the first media, but I wonder if I could also simply transfer the new certificate to my 'expired' boot media? So is there a way to manually change/update the certificate on a boot media?

No you need to regenerate new boot media. You can directly edit the default boot.WIM files with your customizations so that when your certificates expire you dont have to worry about your edits for creating new boot media.Brandon Linton |http://myitforum.com/cs2/blogs/brandonlinton/default.aspx | MCTS - SCCM, MDT, AD