Silly Windows... how to proceed?

[Nolimit]

Soon I'll be formating my HDD and installing Windows 7.
I have 2 HDDs, windows on one, and other one for big files so I'm not going to format that HDD, or rather I can't.
But while I was removing Vista(had some issues) and putting XP(which I'm using now), some windows files somehow managed to get installed on the other HDD... No idea how or why but they just did. And these files are:

$RECYCLE.BIN
Boot
RECYCLER
System Volume Information
AUTOEXEC
boot
bootmgr
CONFIG
gldr
IO
MSDOS
NTDETECT
ntldr

Some of these might have to be there but I'm pretty sure most of them aren't supposed to. (also wouldn't mind knowing if I should get rid of all or what)

So now my question is, if I disconnect that other HDD with these files and format windows HDD, install windows 7, reconnect other hdd, will these files cause problems?
How can I remove them safely?
Hope I was clear enough but here's TLDR verison:

Windows files somehow get installed on second HDD. Want to know how to remove them without formatting that hdd so they dont cause problems when I install new windows.

 

[darknite]

This happened to me a long time ago. When you installed, did you have both drives hooked up? And did you manually make the partitions?
I think I ended up just reinstalling windows with the 2nd drive unhooked. And ever since then that's what i stick to.
So then ya, try doing what you said and see if it works.
Shouldn't cause problems and you should just be able to delete them after the install.

 

[Nolimit]

Both were hooked when I installed it.

So from these files, I can delete them all? None required for hdd to function or something like that?
And will I be able to delete them and if not how to do it?

 

[mlewis]

If you have only the disk that is going to have windows installed on it conected during the install process those files on the other disk will not cause any issues when that disk is reattched. You should be able to delete them without any problems.