This newbie posting clarifies a previous posting and corrects an error. 
Sorry.  

    With your writing about low-level formatting, reinstalling, etc. to make 
space for Linux, I want to make sure that a distinction is clear.  And please 
note that I am not familiar with Windows NT or 2000 and these o/s are not 
included in the comments below.  
    Both chkdsk and scandisk check a Windows hard drive's file integrity.  
Windows will write a given file all over the disc, the end of one block gives 
the address of the next one to read.  An example of a problem that can come 
from this, that chkdsk and scandisk will find, is if two different files link 
to the same target block--this is called a cross-linked file.  A common 
problem when a Windows program crashes and Windows fails to update the disc 
directory for that program is that program data blocks on the disc are not 
assigned to any file nor are they allocated as available: known as lost 
chains.  
    Different is the "defrag"menting process that consolodates disc 
free-space together that had been intersperced with program and data blocks.  
Complicating the defragmenting is the "recycle bin": things that have been 
deleted but can be undeleted.  They are assigned to a special directory, and 
though the file is "deleted" the blocks that the file resides on remain 
unavailable for use yet they show as unoccupied on the defrag screen.  
    To make the space that you can partition for Linux to use, first run 
chkdsk/scandisk to verify file integrity.  Then run scandisk "thorough" to 
verify that the hard disc itself is OK.  Then empty the trash (recycle bin) 
to make disc space occupied by deleted files actually available for use and 
allow other data to be moved into these blocks.  Finally defragment the hard 
drive to gather all of this free space together.  Now you can partition some 
of this free space for use by Linux.

    Next let's put this all together (edited from a previous posting).

  [preparation of the Windows partition for resizing 
            to allow free-space to be partitioned by Linux]

1)  Back-up -  all  (or)  important  (or)  critical  - data   < depending on 
what
          on     tape (or)      CD       (or)   floppy              < media 
you have avail.

2)  Disable anti-virus scanner, screen saver, power management (if active), 
etc.
  <CTRL><ALT><DEL> (once only!) should show the following tasks active
  on Win98 (others should be similar) 
                    Explorer
                    Systray
                    Wsloader
[<CTRL><ESC> on Win3.1 shouldn't show anything (except program manager)]

3)  I always like to run "chkdsk" (without the "") from DOS prior to doing 
anything serious with a Windows HDD (hard drive).  
    Boot to DOS or shutdown to DOS.  Do not run chkdsk while "shelled out."  
    At the "C:" command line prompt type "chkdsk" and <Return or Enter key> 
(again, without the "").  [for simplicity I'll say <Enter>]
    Ignore the scandisk advisory and continue.
    If there are any errors run "chkdsk /f<Enter>" to fix them (as a message 
will instruct).

4)  Within Windows (deactivating other processes first, as noted above) run 
scandisk.

5)  Next run scandisk selecting the "thorough" option.  This may run over an 
hour (depending on hardware).  DO NOT STOP IT unless you are SURE it has 
hung.  If it does hang, cold boot the computer, reset everything as noted 
above and run it again.  And again.  And again.  Does it stop at the same 
place?  Is it getting further each time?  Is there no pattern?  If it stops 
in the same place each time, or there is no pattern you should think 
seriously about buying a new drive (this is the point I bought one for 
myself), though there are drive cables and other things that might contribute 
to the problem.

6)  Empty the trash ("recycle bin") for all Windows users (if individual 
"users" profiles are implimented) and "defrag"ment the drive.  This often 
takes over an hour.  As long as it seems to be progressing allow it to 
continue.  Depending on your hardware, etc., five hours might not be 
alarming.  Proceed as in step 5) if there are problems.  When defrag 
completes successfully, all free space will be consolidated after the 
programs and data.  

    If scandisk completed successfully (even if it took several hangs and 
restarts to get successful completion), defragmentation completed, and upon 
using Windows you do not have operational problems (if you had problems prior 
to the chkdsk/scandisk/degrag process) you can go ahead and shrink the 
Windows partition, and use Linux tools to repartition the now unallocated 
space to create space for Linux to use. 
       If scandisk, etc., completes successfully but Windows operational 
problems continue, do a "refresh" reload of Windows [SEE BOOT FLOPPY WARNING 
BELOW] :  Back-up data, as noted in step 1) above.  Boot from a floppy disc 
and access the CD drive (with the Windows CD already being in place).  
ChangeDirectory to \windows (i.e. if D is your CD drive, first "D:<Enter>" to 
log to the CD drive, then at the D:\ prompt type "cd \windows<Enter>" without 
the "") & type "setup<Enter>" (without "") when you are in the windows 
directory.  This should run a Windows 95 or 98 refresh install and maintain 
your previous configuration and other installed programs, but you MAY still 
have to configure or install periperal drivers (you DO have them on floppy 
don't you?).  The exact results you get will depend on exactly which version 
of Win95 (did you know that there are three, without considering special 
versions for Compaq & other large computer makers?) or Win98 you are using.  
Refresh reloads can also be done with Win3.1.
       If your refresh completes successfully but Windows operational 
problems continue do a full wipe and reload.  Boot from a floppy and format 
c: ... /u << unconditional (forced) format [note that the format program must 
be on and run from the floppy, except with the Win98 install floppy which 
will load utilities into a RAM disc.  
  (If the partition formats successfully you might want to erase this 
  partition [ALWAYS examine all disc partitions first!] with DOS fdisk 
  and create a smaller one for the Windows install.  Leave the unallocated 
  space for Linux to partition later.  Format the new partition, and 
  continue with the Windows install.)  
Change to your CD drive and run "setup" from the root directory.  Do not 
change to the \windows directory.

   BOOT FLOPPY WARNING >>  BE SURE (and I mean to TEST IT FIRST!) that you 
have a working boot floppy configured to access your CD drive  --  BEFORE --  
you refresh install or wipe & reload Windows.  The motherboard CMOS must be 
set to look at A: first!  I advise that you have the DOS format and fdisk 
programs on this floppy disc at the very least.  Write protect this disc 
before you test it.  

    If Windows operational problems continue after a full wipe and reload 
there are two possibilities:  1) the problem is caused by something you 
installed into Windows after the wipe and reload, or  2) you have a hardware 
problem to solve before you can continue with Linux.
 
-Gary-

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