(1) Here is an article I found...
http://www.scoug.com/os24u/2001/scoug012.dfseetutorial.html#:~:text=To%20do%20this%3A%201%20We%20start%20the%20program,anything%20you%20want.%20...%203%20Press%20enter.%20 DFSee -- A Tutorial For OS/2 Users
When you start it, it's supposed to analyze the partitions. I guess they all pass muster, or you'd have said something. I guess, if you ever did the "Back Up, Back Up, Back Up" section, you'd have tried to restore those things. It looks a little scary to me, but can you see how to repair boot sectors & spareblocks with that? (I never heard of a spareblock before.)
(2) You've got no Recovery partition at all. Instead, the Windows partition likely is getting each new WinRE.wim (recovery environment) at C:\Recovery\WindowsRE. So, no repartitioning has been going on during your upgrades. Still, let's see...
BCDEdit /Store C:\Boot\BCD
/Store specifies where to look for the BCD. Without it, BCDEdit complained it couldn't find the "system device". It should show the location of bootmgr which should be C: (maybe referred to as HarddriveVolume3). Also, it should show C as the partition it will load. If that BCD were being used for the dual boot, it would also show a Boot Loader that identifies the eCS partition as D: (or maybe HarddiskVolume4). But EasyBCD shows it isn't a dual boot.
(3) But I guess you are right, there is an IBM Boot Manager on partition 1.
(a) Can EasyBCD show the IBM Boot Loader?
(b) What is the format of partition 1?
(c) Is it hidden like SR?
(d) If you unhide it, can you DIR it?
(4) In a Legacy installation, System Reserved (starting with Win 7). normally holds the boot files including BootMGR. Somehow yours got deactivated & the Windows partition now serves its purpose. That's OK. I think you've got the latest BootMGR. And you probably should be booting through partition 1 anyway which (I believe you) holds the IBM Boot Manager.
(5) You wrote...
"
If you mean on the disk, then yes. It is marked startable and active at this point bypassing IBM Boot Manager. If IBM Boot Manager is used it is marked startable and the 2 partitions Win and eCS are marked bootable.
diskpart dhows eCS as inactive, but again don't care really because IBM Boot Manager controls booting eCS when it is startable and this is how the system worked before failing.
"
That makes me dizzy to decipher. What app allows you to set Startable & Bootable? Is it DFSee? I wonder whether it is talking to the IBM Boot Manager to tell it which partition has the boot files & which has the OS. I wonder whether it also sets/removes the Active status. I think "startable" probably means it holds the boot files. And "bootable" probably means it holds the OS. So, Startable probably belongs on partition 1, & Bootable probably belongs on both the Windows & eCS partitions.
Your Windows partition has boot files, so it can be made startable. I guess the eCS partition does not have boot files, so it can't be made Startable & should not ever be Active.