jubuttib,
To remove the LUNs from Windows:
Make sure nothing is in use using the drives that you want to remove. No programs running from the drives or files opened from the drive
Then take them offline in the Disk Management tool
You can then disconnect them via the iSCSI Initiator tool, but not critical
After you reconfigure your targets, use the iSCSI intiator tool to rediscover the targets. Once discovered, you can bring them online in the Windows Disk Management tool.