hi kernoman, I do have a LS2 with MIPSel and Macronix flash chip (The flashing problem seems only occur in ST chip). After a couple of days studying on this forum. I encourage myself to flash U-Boot and Kernel into my box last night. It works fine with my stock firmware in par(0:1) and Debian 2.6.22ls2 in par(0:3). I mainly follow the steps from Lupin in the famous LNI u-boot and 2.6 kernel HOW-TO post.
I would say, if you know exactly what you are doing. Especially for those danger activities e.g erase and re-fill the flash rom with "erase" and "cp.b". Then flashing U-boot is quite safe. At least you can use U-boot to load the kernel (&rootfs) from somewhere else via NFS in case of non-bootable anymore.
So my suggestion is, check your chip type firstly and then go though the post of following very careful.http://buffalo.nas-central.org/index.php/Information/MIPSelFlashROMhttp://buffalo.nas-central.org/forums/viewtopic.php?f=12&t=3769&st=0&sk=t&sd=a
And then decide whether flash U-boot into your system or just use ram+loader with Christmas tree...
Btw, if you want get help from others, you need tell us more details. e.g. flinfo output(chip type), partation topology...etc