Unfortunately DOS and win9x will assign the first partition of your second psychical disk as drive D, and I don't think that can be changed... I remember trying (and failing) to resolve a similar issue a few years ago. I did find some 3rd party software that could re-assign drive letters, but I could't get it to work.

As Socket3 said, with DOS and Win9x things are somewhat locked in w/o using something like Partition Magic. You can alter drive letters in Win9x but not the boot drive.
Just to clarify: So 1st drive has two partitions: DOS and Win98 (originally C and D). If attach new HD to secondary controller it actually becomes D: (First part of 1st HD= C, 1st part of 2nd HD becomes D, second part of first HD becomes E:). Does that sound correct ? Curious if you Fdisked the new HD on Primary controller without the original attached or on the secondary with Primary still attached ? Personally I fdisk all drives w/o any other attached so any HD could be C: if hooked up by it self, and typically use the BIOS boot menu to boot from the HD I want on motherboards that allow a BIOS boot menu.

Thanks for the replies.

I kinda remembered it from the nineties (and eighties) 😀 to be as Socket3 said. Yes, Horun that is exactly how it went down. The new drive as primary slave took over D (and F?) I think.

Any ideas to get this move or cloning to new hard drive solved?

-One possibility would be to get some external IDE cloning hardware dock for my Windows 10 main PC (I already have some old USB drive case that can attach to IDE) and transfer the images there.
-Or then just reinstall the whole DOS and WIn98 for the new drive in LBA mode. This takes some time and patience though and does not sound like a good option.

Anyways if you want to use a larger hardisk and have more storage, you're using fat32 and dos 6.22 can't work with fat32.
As I recall the bigest partition you can make with dos 6.22 is 8gb, and if you want multiple partitions than the total sum of all partitions is no larger than 8gb.
so how were you planing on partitioning the new drive. so that it can work any different if you want to use dos 6.22

No matter what you do you can only have 1 primary partition if you want to run the computer that way,
and because you chose to use dos 6.22 that means you are constrained to 8gb.

You might be able to work around this by using independent disks. Run 6.22 on the old one and then install 98 on the new dirve with fat 32.
Then you can have multiple primary partitions on seperate drives.
Caveat to that is 6.22 wont see the fat 32 drive at all, but 98 should be able to read the 6.22 just fine.

That is the simple way to do things.
More complicated way to do things is install a boot manager like grub or ranish partition manager and run multiple primarys on the same disk.
then you can have a 8gb dos 6.22 partition and fill the rest of a drive up if it is like 32gb? with a primary fat32 partition.
Thats the only way.

Thanks guys. I ended up doing a reinstall after copying some stuff to safe on a modern pc.

The only choice here was to do only one 2GB dos partition which dual boots on same drive to FAT32 Win98SE. Then just add the FAT 32 partitioned second drive.