You just flash u-boot image without any kernel attached, either using flasher3.5 from desktop, or - more useful way, as it is independent from other devices - using flasher on device itself, as described here:
http://wiki.maemo.org/Overclocking#F...rom_X_Terminal

(while most info on that wiki page is completely outdated, flashing from terminal section remained actual, to this day).

Just be sure to do *both* commands as root. You can take u-boot image from uboot-booimg package - download it (*not* install, just download), unpack via dpkg-deb -x /path/to/download-u-boot-bootimg.deb /home/user/MyDocs, and you'll find image in one of extracted folders (u-boot.bin, IIRC).

Anegdote - using this method, I was able to remotely migrate device from multiboot to u-boot, without physical access to it (it was many kilometers away), and no one touching it - in addition, device was sitting behind NAT and firewall, that I had no access to. Everything was done via ssh (two sessions for flashing), and automatic reverse-ssh upon device reboots. No local intervention of anyone was required

/Estel