Trying to boot El Capitan, High Sierra, and Win7 UPDATE: 
Thank you for your responses and helpful ideas! I was able to fix the Mac-related issues by upgrading to Sierra - not High Sierra - which can support both Logic Pro 9 and Logic Pro X 10.4 concurrently. This is not stated at all on Apple's site. 
At any rate, I was able to now only need a Mac partition and a Windows partition. I have had some other catastrophes to deal with in the meantime, so I have not had the time to fix the Windows side of things yet. I will report back when I do!

I'm going to try to run down this issue as succinctly as possible, but bear with me; it's convoluted. 

Last year my main 1TB HDD in my mid-2010 Mac Pro showed signs of failure. I proactively bought a new 2TB SSHD, made an image of my El Capitan Mac partition, and did the same with my Boot Camp Windows 7 partition. I formatted and partitioned the new drive appropriately and restored those images onto the new drive. 
MacOS worked great, but the Bootcamp partition refused to boot, no matter what I tried. However, I could still boot into Windows from the old drive just fine, so I left it in the machine. I ended up using a Windows program to repartition that drive into its own Windows drive, using the entire 1TB. 
I left the Bootcamp partition intact on my new drive in case I figured out how to fix it. 

Another weird quirk of this configuration is that when I am booted into OS X, I can't see my Windows drive at all. It shows up in Disk Utility but is completely unreadable. However, when I am in Windows, I can see all my Mac drives as normal. 

Fast forward to yesterday. I am a music producer and game composer, and the project that I'm working on would really benefit from me upgrading to the latest Logic Pro X from my current Logic Pro 9. 
Logic Pro X 10.4 requires High Sierra.
Logic Pro 9 does not work in High Sierra.
I need both for backwards compatibility reasons; Logic Pro X ditched the 32-bit bridge, and I still have many projects in progress that use 32-bit plugins. 
I need both. So I just finally ditched that Bootcamp partition that didn't work, cloned my MacOS partition, booted into the cloned partition, upgraded to High Sierra there, got the new Logic working.......

And now I can't boot into Windows. 
It's on a separate hard drive! I thought this would circumvent the 4 partition limit. 

To clarify and summarize this issue, my main hard drive now contains two partitions; one for El Capitan, and one for High Sierra. I have a separate HDD that contains Windows 7 which was originally set up via Boot Camp Assistant, but went through the aforementioned changes. 
I need to be able to boot my Mac Pro into any of these three OS'es at any given time. 

What in the world can I do? Can I finally have some peace and harmony in my computing life for once? Has anyone encountered anything quite like this? I'm pretty frustrated.
Generally, when you move Windows, you have to rebuild the BCD file.

Windows generally looks at the contents of a partition in order to determine the partition type. The macOS operating system relies on the type information stored in  the respective partition table. So it is possible Windows could boot even though the partition types are wrong. On the other hand, macOS would not not be able to read the same incorrectly typed partitions.

Each of your drives have two types of partition tables. Windows 7 uses the legacy MBR partition table and macOS uses the Guid Partition Table (GPT). So it is possible for one operating system to see the partitioning differently than the other operating system. 

Fast forward to yesterday. High Sierra has a tendency to reset MBR partition tables to what is referred to as a full protective MBR (PMBR). I layman terms, High Sierra may have erased Windows 7. Normally, this is an easily recoverable event, but I this many not be true in your case. To determine the damage, one would first have some detailed information about your current partitioning.

I am not familiar the Mac Pro model, so I may get some of these commands wrong. None of the commands alter your Mac. The commands just provide information about the partitioning and volume formats. Edit your question and add the output from these commands. If necessary precede a command with sudo.

diskutil  list
sudo  gpt  -r  show  /dev/disk1
sudo  fdisk  /dev/disk1


I believe you have to boot to macOS Recovery to execute these next commands.     

gpt  -r  show  /dev/disk0
fdisk  /dev/disk0