The OS X 10.7 upgrade should work independently of your Boot Camp installations, but some people may find that after upgrading to Lion their Boot Camp installations are no longer accessible. In some instances the Boot Camp partition will disappear and will not show up in the start-up disk preferences or in the Finder. In other instances the volume may still be present in OS X but will not boot when attempting to load Windows. The reason for these problems may be as simple as an improperly configured driver or because of custom partition configurations on your boot drive.
NTFS driver configuration
Apple's OS by default can read NTFS partitions, allowing you to browse through your Boot Camp installation and copy files to your OS X partition if needed; however, to add full NTFS support for reading and writing to the drives you can install third-party drivers such as Paragon NTFS, Tuxera NTFS, or the free open-source NTFS-3G driver. While these drivers should work in Lion, some people have had issues with their configurations after upgrading, and have found that uninstalling the drivers have allowed their broken Boot Camp installations to begin working again.
MacFixIt reader "Paul" writes:
I've recently upgraded to OS Lion and found that my Windows 7 Bootcamp partition has stopped working and I can't mount it within OS Lion...I discovered the problem. I had installed Paragon NTFS read/write software on my computer, which didn't work with OS X Lion.
If you are experiencing a problem in which your NTFS-formatted drives, including Boot Camp, are not showing up, then try uninstalling any third-party NTFS drivers. If you need the functionality of the drivers, then you can try reinstalling the latest version of the driver to see if it works, or change to an alternative one.
Beside odd problems with NTFS drivers, some people may have problems in which the Windows volume will show up and be browsable in OS X but not be bootable. This is likely an issue with the partition configuration of the drive. In order to boot Windows, the OS will need to be on one of the first four partitions on the disk. Some people may have set up their disks to have OS X followed by several partitions for data storage or backup purposes, and then had Windows installed on the fourth partition. In this setup, if you upgrade to OS X Lion when the OS creates the recovery partition, it may shift the Windows partition to be the fifth partition on the drive, resulting in it no longer being able to boot.
If this is the case, then you can try removing a partition that resides before the Windows partition, by backing up its contents and then selecting it in Disk Utility and deleting it. Be sure to back up your entire system before doing this, as modifying the partition tables of a system can result in data loss if the process goes awry. To do this, once the backup is created, go to Disk Utility and select the disk device. Then click the Partition tab, select the partition that is above the Boot Camp installation, and delete it by clicking the minus button. Do this for other partitions until the Boot Camp partition is the third or less from the top (to account for the hidden Recovery volume), and click Apply.