Will not boot except through recovery - every time

After having trouble with the Fall Creators Update not installing, I finally got it to install, but my computer would never shut down afterwards. I foolishly forced power off, and now am stuck with a bizarre boot problem, which I'll describe as well as I can below.

My system:
Alienware laptop with an M.2 SSD installed as boot device with Win 10. It also has a rotating HDD for data. The BIOS screen shows both drives installed. UEFI boot.

Symptoms:

• On every boot up, I get the blue screen error 0xC0000098 for missing BCD file.
• If I hit F12 for boot options while starting, I can see that the Windows Boot Loader option says it's on the HDD (which doesn't actually have an OS - hence the BCD error). There is no option for Windows Boot Loader on the disk with the SSD.
• If I plug in a USB recovery drive, I can boot to that and choose "Continue" and it loads Windows ok. (Odd symptom - it consistently shows my login screen twice; I enter my ID/pwd on each and then get in.)
• Once loaded, I can confirm that the SSD is accessible and appears to have all the files on it, including Windows and my applications.
• In Windows, Disk Management shows Disk 0 (the HDD) as healthy and Disk 1 (SSD) as healthy with boot partition identified. That's consistent with what it said when everything was working fine.
• Also from recovery, I can select "Use another OS", which shows me TWO selections that both say "Windows 10 on partition 9". Both of these work like choosing "Continue", in that I eventually get to a running state.
• Another possibly unrelated issue is that Chrome won't run anymore. I launch it, it shows up in the Task Manager, but never fully launches. Not sure if this is related or coincidence.

What doesn't work:
From Recovery / Advanced / Command Prompt:

• Running bootrec /scanos only finds windows.old on the SSD, but not the current windows installation
• Running bootrec /fixmbr returns "cannot find the file specified"
• Running bootrec /fixboot returns "cannot find the file specified"
• Running bootrec /rebuildbcd states that it can only find windows.old on the SSD and then errors out with "cannot find the file specified"

System Restore to the point just before the Windows Creator update failed, possibly because I can't get a clean boot.

At this point, I am at a loss of what to do next. It seems like all my files and the OS are still there, it just won't use them to boot. Perhaps the boot configuration is missing/corrupted and doesn't point to the SSD, where the OS actually is, but I can't figure out how to repair/recreate them. Or, key OS elements are actually missing, but that seems less likely since the computer eventually works once I boot it through Recovery.

Any help y'all can provide?

Thanks,
Scott

TopGunDCP,

Here is the info you requested. Obviously, Disk 0 is the rotating HDD; Disk 1 is the M.2 SSD.

1) Please update the system specs in the "My Computer" section:
How To Fill Out Your System Specs
System Specs - Fill in at Ten Forums:
System Specs - Fill in at Ten Forums Site Use Tutorials
In the left corner below in your post you find 'My System Specs'.
After clicking it you can find a link a little below that says 'Update your System Spec', click on this link to get to the page where you can fill in your system specs.
System Info - See Your System Specs - Windows 7 Help Forums

Include PSU. cooler, case, peripherals and anything attached to the computer by wired or wireless (mouse, keyboard, headset, printer, xbox, etc.)

2) If possible please download and install Minitool partition wizard and post an image into the thread:
Best Free Partition Manager for Windows | MiniTool Partition Free

3) Open administrative command prompt:
Administrator: X:\windows\system32\cmd.exe
4) type: bcdedit | find "osdevice"
5) type: C:
6) dir
7) type: D:
8) dir
9) post an image into the thread

Topgundcp,
A couple of questions... first, how does the redundancy help? There are no OS files on the HDD, only on the flash. What is going to be redundant?

Also, it sounds like this will be non-destructive to the files on both disks; it that correct?

Finally, you were mostly correct in your assessment. I did use EaseUS partition manager and to-do backup to clone the OS install when I added the SSD. However, this computer never had Windows 8/8.1 on it. It was purchased new from the OEM with Win 10 already in place. Does that change anything about your recommendation?

Thanks so much for your help!

Zbook,
I'll pull that additional data this evening. Thanks!

Since you want the HDD to contain only data, I would use MiniTool Partition Wizard Free to delete every partition on disk 0 except for the D: drive partition, then expand the D: drive partition in both directions to fill the drive.

Kyhi's bootable recovery tools has multiple partition programs that will let you do that, and it also has Macrium Reflect Free which is very good at repairing Windows booting problems.
Windows 10 Recovery Tools - Bootable Rescue Disk - Windows 10 Forums