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Disk Utility should be able to wipe out any existing partitions before attempting to install a new OS, but my favorite fallback is to use a Windoze PC to 'clean' drives to get back to basics before a new install. If you have access to (almost any PC with a USB port) and you have a USB to SATA cable to plug-in a bare drive externally, then I start by right-clicking the start menu to get to the legacy start menu and then select Disk Management. Disk Management is like Mac's Disk Utility, but I use it first to get an overview of the drive(s) before starting. The takeaway there is usually visible to the left where it shows you the disk number assignment(s) by the OS. The boot volume will usually be Disk 1 and the external (or other) drives will be 2, 3, etc.

While keeping Disk Management open, go to the taskbar and type: cmd to launch a terminal window (aka DOS command interpreter). At the prompt type: diskpart - which will usually open a new window with a different prompt. At that prompt type: select disk 2 (assuming your recycled drive shows as that number in Disk Management). Make certain that you have selected the correct drive (measure twice/cut once) and when confident type: clean and press return. At this point you can close the command prompt windows and the Disk Management window will now show the drive you just wiped as uninitialized. At that point you've blanked out the drive and back on the Mac you should see this reflected in Disk Utility. If you use Disk Utility to initialize the drive it would be advisable to start by formatting it as a GPT (GUID Partition Table) first (MBR is now the best option for bootable flash drives) and then creating Mac partitions as needed. You will probably want to use APFS for SSDs but Mac HFS works fine for spinning media.

My cMP 3,1 has a 1.92TB Samsung SSD that I have multiple partitions on. The primary (450GB) partition is now Sequoia, and I also have legacy Mac HFS partitions for High Sierra and Mavericks with the remaining space formatted as a Mac HFS data volume. This configuration is not without some problems. I upgraded the original GPU to an inexpensive used metal-compatible RX570 which OCLP provides the means of loading kext drivers so once the EFI partition is loaded at startup provides a boot picker that now allows all three OSes to display and load. I had originally used dosdude1s patcher to get High Sierra to load and ran it again on the Mavericks partition to get his kexts to let me almost use Mavericks. I say almost works because the RX570 is not actually recognised correctly by the OS and without the original GPU acceleration and VRAM some legacy apps (like Apple Compressor) do not work yet and I have little hope that there will be a solution other than swapping out the GPU with the original card if I need to go back.
 
I put a brand new ssd into the MacPro 3.1 and installed El Capitan from my boot thumb drive. This worked well and El Capitan is back running on my computer. Unfortunately, I now find that two of the 3 drives (that were working well before I started all this) are no longer accessible. They do not appear on the desk top or anywhere else I can see, except that they are indeed listed in Disk Utility. Disk Utility says that they are both full, although they are really not full. I'd really like to access these drives but I don't know how to do it. Suggestions will be greatly appreciated.
 
The two disks that I can no longer get access to are the two that I tried to install Monterey with the OpenCore Legacy Patcher. I've run disk utility repair on both but it did not help. Again, I can see the disks in Disk utility, but I cannot see the disks from the rest of the mac. Bummer. I want the files on those disks.
 
I want the files on those disks.
Chances are slim, but there are a number of paths to a resolution of your issue either way.
First off, did you leave the Time Machine disk untouched or at least, can you still see your previous instance states from before the upgrade attempt in Time Machine?
 
Chances are slim, but there are a number of paths to a resolution of your issue either way.
First off, did you leave the Time Machine disk untouched or at least, can you still see your previous instance states from before the upgrade attempt in Time Machine?
Yes, indeed. The back up disk looks fine. I have not tried to open time machine but I'm hopeful that it will be able to bring back my files. The two disks that I cannot see were both used as targets to install Monterey with Open Core Legacy Patcher. THat is probably what did them in. I've not used time machine ever before but will study up on it before I try to use it. Thanks for the idea.
 
I've not used time machine ever before but will study up on it before I try to use it.
You basically need to boot into recovery and select the option to restore from Time Machine there. That is, not from Mac OS itself. Starting up a Mac OS USB install disk should bring the recovery options up. Since you have recently reinstalled El Capitan, you might still have the install disk you created. If so, start this up to get the restore option.

Use Disk Utility to prepare a volume to recover to beforehand. Disk Utility will also be available when booted into Recovery. You might want to ensure your new reinstalled El Capitan instance has a different name to the original one.

If you can't get into Recovery because your GPU cannot show the screen, there are ways around this. I think it should show up in most cases but a bit hazy on that part now. I actually got into using alternative tools for booting mainly because I was concerned about recovery access to Time Machine when I first updated my GPU to one without native boot screen.

I think it turned out to not be an issue but I forget now. In any case, there are tools that will ensure the screen is shown on almost every GPU and I had started using one of such. I my case also, I actually decided Time Machine was not the best option for me and i started using Carbon Copy Cloner, which allowed access from Mac OS.

I digress though. Main thing going forward is to always ensure you never overwrite your working setup or that you back such up before overwriting.

After you hopefully get El Capitan restored, can look again into getting the newer unsupported versions in place.
 
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