Hey,
I have this very same problem, after upgrading to Yosemite I lost my Windows 7 which I installed on the bootcamp-partition.
On this partition I had directly installed with a build-in partition of 25gb and afterwards I added another 25gb due tolater apps I had to install which I didn't think of at the time of setting up the partition in the first place. I did this throughout 'disk-utility' and rendered 25gb unclaimed by either partition and then in the bootcamp using a wizard. (an app vouched for in the walkthrough on Youtube) What's interesting though was that after upgrading the 25gb I later added was send back to macintoshHD (the original partition) and the other one as you've read before was a damaged 'Disk04'.
To repair the remaining 25gb I accepted my losses and first deleted the contents of DISK04 and also deleted something else from it within 'Disk-utility' now it re-named itself to '04' and then later i clicked the main partition (in the bar left you have 2 sub-partitions and the main partition should still be called macintoshHD). There I deleted the entire 04 partition and the remaining 25gb that was first lost found it's home again.
I get that most of us probably want to rescue their partitions but I've been toughened by windows and the rough edges of bootcamp and already know it would either be a lost effort or take double if not triple the time needed to just install it all overnight.
Best of luck all, hope it works!
BeyondJupiterHD (Christophe)
