You have two installations of W2K; one on the c: drive/partition = winnt, and another on d: partition/drive = winnt.
The version in c: has the line in the boot.ini which refers to partition(1); the version in d: has the line which refers to partition(2).
Since each installation is on a separate drive/partition each goes in as winnt. If they were both in the same partition/drive then second to arrive would be in as windows.
You say the second version is buggy. When you refer to second version do you mean the version on d: ?
Presumably you are OK booting to the version on c: (which is set as the default OS to boot) and are happy to lose the version on d: (partition(2)?
If so leave default OS to boot as is, and boot to version-1 on c: (i.e. partition(1). Verify it is set as default OS to boot. Then locate/delete the winnt folder from d: drive/partition (via W2K Explorer). Also remove the line that refers to it in the boot.ini.
Reboot to ensure all is well with version on c: . Presuming so... (it should be) empty recycle-bin and defrag d: drive/partition to tidy up the scene.
Job done.
Leave data in d: whenever possible; data in its own space (away from OS/apps/utils) is preferable (safer) than having an all-in-one partition/drive...
To clarify boot.ini clean-up/editing, remove this line (only):
multi(0)disk(0)rdisk(0)partition(2)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
It refers to partition(2) - the version of winnt on d: .
And again you delete the winnt folder from d: (not from c: ).
NOTE:
The above info/details presume that the version on c: is the one you wish to retain. If the version on d: is the one you wish to retain - post back before going any further.
I can see no reason to reformat d: etc... Once winnt has gone from d: partition/drive that space is free for data etc. All that is required is to defrag it?
Expanding c: at the expense of d: via PM or SC is an option; but on occasions folks have had problems doing it with the NT family of OS... If you decide to go that route, then back-up all data totally - first - off the drive (CDR/RW). Better safe than sorry. (Also you might not have adequate free space on c : for all the data on d: ?)
If you have a shortage of space for additional apps/utils on c: remember that many can safely be installed to d: (i.e. the apps/utils files themselves). The registry on c: will point to them as being on d: when they are required to run via the OS on c: .
This is ruse is sometimes used when installing the same app/util to each OS in a dual/multi-boot environment. It saves drive space as only registry entries and required dlls etc. actually go into the individual OS/partition; the bulk of 'common' files share the same (non-OS) partition. Most apps/utils will allow this, although some (often M$) may not be so helpful/obliging; it's all a matter of luck?
This latter option would remove the need to resize c: at expense of d: (with it's possible irritations/risks)?