I couldn't find any good search results on how to remove an active partition on a Windows system (and this is not in the disk management GUI) and eventually figured this out on my own, so I thought I'd share. Of course, this is only useful if you have a drive which no longer contains an operating system / boot files and you just want to remove the flag. The solution is simply the command-line tool "diskpart" which resides in the windows\system32 directory and the Inactive command. the active command marks it for active, which can also easily be done in the disk management UI.
DISKPART> help inactive
On disks with master boot record (MBR) disk formatting, marks
the partition with focus as inactive.
The computer may start from the next option specified in the BIOS such as a
CD-ROM drive or a Pre-Boot eXecution Environment (PXE)-based boot
environment (such as Remote Installation Services (RIS)) when you restart
A partition must be selected for this operation to succeed.
Your computer might not start without an active partition. Do not mark
a system or boot partition as inactive unless you are an experienced
user with a thorough understanding of Windows storage management.