@Scott Haven't worked much with Win 2000, thankfully.
Tried to reproduce your problem in my lab by installing Win 2000 Professional on ESXI, adding a bunch of virtual HDDs using FAT or NTFS with basic or dynamic disks (trying to see if some combination caused it to fail), downloading the VMDK files, converting to qcow2, and importing into Proxmox.
However wasn't able to make it past the converting VMDK to qcow2 step. I must've messed up somewhere because after importing the disks into Proxmox I just get a Windows "boot drive inaccessible" error.
Sadly I didn't take many notes while experimenting with all this, but if you end up finding a solution I'd be very curious to learn it.
The only part that stuck out to me while doing this is that when initializing new disks on Win 2000 it seemed to default to dynamic disks, and was trying to build a software raid by default. I'm not sure if this would be a factor with your disk conversion - but I can see how if the disks are configured as a raid but "qemu-img convert" is handling the disks one at a time it could have strange results.
bash-5.1$ qemu-img convert -p -f vmdk -O qcow2 Chris_Win2000.vmdk Chris_Win2000.qcow2
(100.00/100%)
bash-5.1$ qemu-img convert -p -f vmdk -O qcow2 Chris_Win2000_1.vmdk Chris_Win2000_1.qcow2
(100.00/100%)
bash-5.1$ qemu-img convert -p -f vmdk -O qcow2 Chris_Win2000_2.vmdk Chris_Win2000_2.qcow2
(100.00/100%)
bash-5.1$ qemu-img convert -p -f vmdk -O qcow2 Chris_Win2000_3.vmdk Chris_Win2000_3.qcow2
(100.00/100%)
root@MGV7091:~# qm importdisk 102 Chris_Win2000.qcow2 local-lvm
root@MGV7091:~# qm importdisk 102 Chris_Win2000_1.qcow2 local-lvm
root@MGV7091:~# qm importdisk 102 Chris_Win2000_2.qcow2 local-lvm
root@MGV7091:~# qm importdisk 102 Chris_Win2000_3.qcow2 local-lvm