Not on a NT to XP upgrade - that does not save files against an
uninstall, so I don't think the entry will appear. If it does, then
taking it offers a choice of uninstalling XP or removing the backed up
files.
Aside from this, the upgrade ought to have been done by running from the
NT and taking Upgrade - that should not leave NT files around. If it
were done by doing a New Install and setting up a dual boot, then it
should have been done into a Windows\ folder, while the NT will be in a
WinNT\ one that will no longer be used. If that is the case, then
delete that WinNT\ folder, and then run MSConfig.exe. On its Boot.ini
page click 'Check all Paths', which will find the NT one no longer valid
and offer to remove the entry from boot.ini