I have just upgraded to El Capitan from Yosemite.
Previously when holding down the option key I had the option to boot into Windows as I had installed this using Boot Camp. Now it doesn't give me that option.
After installing El Capitan I used the partition tool in Disk Utility to create some free space (the idea being that I would download Mini Tool partition wizard once back in Windows and get some more space). The Bootcamp partition seems to be there as you can see in the screenshot pictures but it just doesn't give me that option of booting into Windows when holding the alt key at start up anymore!
I changed the start up disk to Bootcamp (Windows) on start up but came up with this message "No Bootable device - insert boot disk and press any key." When press alt key can still only select Macintosh HD. It's Windows 7 and all the installers still seem to be there when I select the bootcamp disk.
Tried turning off the System Integrity Protection (SIP) as recommended by @DavidAnderson but when back in El Capitan it still didn't give me the option to 'first aid' the disk.
Here's what it currently looks like in Disk Utility...