Boot Camp Windows partition lost after El Capitan upgrade I upgraded through App Store, and after the upgrade, the boot select screen no longer shows my Windows partition, nor the recovery disk. Running diskutil list yields the following: 

/dev/disk0 (internal, physical):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *320.1 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage Macintosh HD            222.0 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data                         39.0 GB    disk0s4
/dev/disk1 (internal, virtual):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           +221.6 GB   disk1
                             Logical Volume on disk0s2
                             9678D097-D642-4108-813B-E10AF9578FE3
                             Unlocked Encrypted


Disk Utility first aid passed with no error. 

As far as I can remember, I allocated 100GB or so for the Windows partition. Now I wonder how I can get that back without reinstalling a clean Windows.

Running gpt shows the following:

gpt show: /dev/disk0: Suspicious MBR at sector 0
      start       size  index  contents
          0          1         MBR
          1          1         Pri GPT header
          2         32         Pri GPT table
         34          6         
         40     409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
     409640  433593744      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
  434003384    1269536      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
  435272920  113699624         
  548972544   76169216      4  GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
  625141760        655         
  625142415         32         Sec GPT table
  625142447          1         Sec GPT header
Since I need to work with both operations urgently, I have wiped out the entire 320GB drive using an OS X Yosemite startup USB.