I have a MacBook Pro that dual-boots Ubuntu 12.04 and OS X Snow Leopard. I'd like to upgrade OS X to Mountain Lion, but have never done this on a dual-boot OS X system before. Will the upgrade work safely, or is it to likely to mess with the EFI stuff and my partitions?
I did the same thing about four days ago, but the upgrade was from Lion to Mountain Lion. I also have done the same with Snow Leopard to Lion. I have a triple boot with windows 7, ubuntu 12.04, and osx, with refit (which I highly recommend installing if you haven't already). All of this on a MacBook Pro 5.5.
How I upgraded was through the app store (downloaded, and then clicked open the file and told it to install. I did not upgrade through making a DVD or usb, and it was not a clean install, so I can't say if that will some how change things.) and it worked perfectly fine for me. I'd be interested though to see if anyone has had issues like that before.
But, hope this helps ease your worries. If anything just be safe and back everything up of course.
I'm going to answer my own question, as it was not a straight-forward process, but it all worked safely in the end.
At this point the installer ran and let me select the newly resized partition. The partitioning for my dual boot setup meant that the installer warned me that "Some features of Mac OS X are not supported for the disk Macintosh HD", but that as OK and the installer ran fine.
After this Mountain Lion was installed fine but my rEFIt boot menu had vanished. This was an expected part of the update process (as documented here) and I just had to run
and the menu was back at the next restart.