In my previous post I enabled BitLocker on both my partitions (Link). The trick now is to reinstall Windows without decrypting the system. In this example my data is stored on the second partition (Data Partition or D:) and that partition is encrypted and must be preserved.
When booted from media. The installer is asking on which partition it will install Windows. Because BitLocker has encrypted the old system partition, we aren’t able to format the partition. Just delete the partition, recreate it, format and install Windows. (Do not touch the data partition). If you want to preserve the data on the old system partition, you have to recover that partition. (Hmmm new post will come in the future 
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| When the installer is ready and Windows runs normally. Open the Windows Explorer.
As you can see, the Data partition has a nice looking icon. But is not accessible. |
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| Right click on the partition and choose: Unlock Drive. |  |
| Insert the USB flash drive.
Click on: Get the key from USB flash drive. |
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| Select the drive on which the key is stored. Click: Next. |  |
| Now click on Manage BitLocker. |  |
| It’s not possible to automatically unlock the drive, because the system partition isn’t encrypted. (Read my other post howto do this: Link)
Click on: Add a password to unlock the drive. |
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| Give a nice strong password and click: Next. |  |
| Your done.
Click: Close. |
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| Now the partition is accessible. |  |
Encrypt the system partition and you are able to automatically unlock the partitions at system boot.
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