Missing/moved directories in Win 98

When PC running Win 98 was booted up several error messages came up saying that shortcut targets were missing. These executables have been loaded everyday as normal bootup such as the palm desktop hotsync manager, zone alarm firewall, etc. When I checked for the targets I found that several directories are missing! Particularly a directory on a second disk drive named D:Programs is missing. This contained many programs not critical to Win98 OS but still necessary for business tasks. Outlook also is missing some dll files. Can anyone help, please?