The drive flashing amber and green is normally indicating a Predicted Failure on that drive. Is the drive rebuilding the one flashing or is it another drive? Also, is the drive showing a YES below Failure Predicted in the Physical Disks page?
If so then I would suggest stopping the rebuild as rebuilding a Predicted Failure drive can cause a punctured strip / double fault on the Virtual Disk. If the drive is already rebuilt then don't simply remove the drive if it is showing as ONLINE, as this can cause issues as well. If the Predicted Failure is ONLINE, then you will need to Force Offline that drive before removing, and then replacing.
Let me know what you see and how the drive is currently flagged.