Shortly after installing the Fall Creators Update I had issues shutting down(even with fast boot off), this eventually became problems starting up. The computer would hang only saying "just a moment". This does not seem like a Linux problem but I have had problems with updates before so on a hunch I disconnected my Linux drives and it powered on and off perfectly fine. Does anyone else know about this? Do I have to reconfigure Grub2?

Problems shutting down what, you windows system? Which windows do you have, 10? I think you would have better luck doing an online search for problems after installing the Fall Creators Update for windows or posting on a windows forum. Not sure how you made the leap to a problem with Grub2.

I have seen reports where the update added a new partition, and so messed with Linux systems. I would expect that using separate disks wouldn't suffer the issue - and UUIDs would also presumably be fine. Hard to know the exact problem.

The fix was usually to re-install grub from a liveUSB. Fire up your favourite search engine.

Well yancek since Windows boots and shutdown with the disk removed, it's either the IDE driver(yes I still use IDE) or Grub. I think Grub is more likely. MS goes very far to make sure older tech still works.

I am going to try a 'boot-repair' disk, which is a live CD that comes with a program that can fix common Grub issues. I'll let you know how that goes.

If you use the boot repair disk, use the Create BootInfo Summary option and post the link you are given rather than trying to make repairs.

In your initial post, you indicate the problem began with difficulty shutting down windows which would be unrelated to Grub. Boot repair should provide some useful info, CSM/Legacy or UEFI, EFI partition information, boot files and more.

I can't seem to use it in either case. It can't download Fedora packages. It also seems built for EFI and I have a BIOS. Here is the file it produced: https://pastebin.com/eAd3R8VU

What exactly is the status now? Can you boot both windows and Fedora and booting is slow on one/both?
You have Grub installed in the MBR on sda (298GB drive) and the correct grub files are there. I don't use Fedora so I'm not sure if it is standard to have both /boot/grub/grub.cfg and /boot/grub2/grub.cfg but apparently /boot/grub2/grub.cfg on sda1 (hdo,msdos1) is being used.

If you look at the grub.cfg file under /boot/grub2, it has proper entries for Fedora but no windows although a windows entry is shown in 30_os_prober. Both of these entries point to sda1 and that isn't right. According to boot repair, your Fedora is on sda1 (that's the 298 GB drive) and windows is on sdc (465GB drive).

If I understand correctly, if you boot the windows drive, no problem but if you boot from sda(298GB drive) you have problems. Is that correct? You might try booting Fedora and running grub-mkconfig to create a new grub.cfg file with the windows drive attached obviously. Not sure how things got the way they are with both Fedora and windows entries pointing to the same partition. Don't have any other ideas.

I did not rewrite grub last night, so things should be as they were. I can boot Windows and Linux but on Windows, it freezes at "just a moment".

I opened GParted from Fedora, sda1 is Windows(465 GB). Sdb1(298GB) is Linux. Bios boots from the "sdb" drive. The MBR on SDA(465GB) runs Windows not grub.

It seems these days all drives use a "sd" prefix although "sda" is the only SATA drive, the other 2 are IDE. I don't know if that matters.

I had Grub 1 at one point so I might have some legacy files.(my Fedora install has been around since at lest Fedora 14)

With this info in mind, what do you think I should do?

It is imperative to keep the WinRE partition after the Windows 10 partition. We need to stop advising folks to shrink Windows to make space for a Linux install, as this will put Linux between Windows 10 and the WinRE partitions.

When Windows 10 applies a cumulative update such as the creators update, it is similar to a service pack in older versions of Windows, basically upgrading most of it or similar. When it does this type of update, it also has to rebuild the recovery environment in the WinRE partition, if that partition is not beside it like it is supposed to be, it will shrink it's own partition and create a new WinRE immediately after it even if the original WinRE is after the new Linux partitions, as a result the partition structure and number of partitions change. It needs the WinRE beside it in case it needs to enlarge the WinRE in which case it will shrink itself to enlarge the WinRE.

So...
Make sure WinRE is always after the Windows 10. I learned the hard way and spent a long day fixing things after the Creators update.

As for the OP's problem, because Windows practically rebuilt itself, and the computer is UEFI, it may have assumed it would automatically be booted EFI mode. Lines 1079 & 1080 of the boot repair output shows something EFI, is this normal when it is installed in legacy??? I don't know, but I have a feeling this is the problem. When you remove the Linux drive, it boots the Windows drive in EFI mode.

It may be best to re-install/redo everything and just stick with the future and get used to it, because this is not likely to be the last cumulative update. Install in UEFI mode, convert the drives from MBR to GPT, it works good.

Is this when you boot windows from the Fedora Grub? I would not expect there to be any problem when you boot the windows disk as it has windows code in the MBR and only windows on the drive.

Rename the grub.cfg file in /boot/grub2 to grub.cfg.bak just in case something goes wrong as it does actually boot. Then run from Fedora the grub-mkconfig command as root. The Fedora site at the link below explains how to do that. If creating a new grub.cfg menu doesn't improve things or is problematic, you can always delete the new grub.cfg file and rename the old grub.cfg.bak to grub.cfg. Obviously, have both drives attached when running the command. Is the 232GB drive just a Linux data partition?

https://fedoraproject.org/wiki/GRUB_2

You don't have any Grub Legacy files, just Grub2 in two different directories. It might be that Fedora made a change in the last few years and now uses /boot/grub2 rather than /boot/grub, I'm not sure.

Yes

I'll give what you say a try.

You may also get away from re-installing by using bcdedit in Windows to revert to legacy boot, which would rebuild the first sector of it's partition, possibly the first sector of the drive also which would also be necessary to boot that drive with grub.
EDIT: But might this method screw up grub???

I just tried telling BIOS to boot directly from the Windows drive and it did not work. The other drives were plugged in, that means it's not a problem with Grub but the way Windows is booting.
I will now report this problem on a Windows forum.

+ 10 points to Linux, I have never had an issue like this on the Linux side.

Windows 10 default is UEFI, you have a UEFI computer. It's not Windows fault you are using legacy.
Look into reverting Windows to legacy, then boot a Linux live CD or Fedora install CD to re-install grub in Fedora in a chroot and then update-grub.

EDIT: Or, leave Fedora and /home drives disconnected when reverting Windows to legacy boot, then grub should still work to boot Fedora after plugging the drives back in. Then try re-installing grub to hopefully get rid of excess files, then update-grub to get Windows in the menu proper (OS-proper)