As Win98SE is still my favourite OS, I've decided some years ago, I will always use a boot manager I can access and control from it and DOS as well.
Also had quite some trouble with LILO in the early years.
And more than once, I've had a Linux CD with bad behaviour, partitions and boot manager related.
So I am using the boot manager, that comes with XFDISK, my favourite partitioner for years.
It resides in the MBR of the first physical HDD, could be removed easily by FDISK MBR.
Linux start routines are advised, to reside in the boot sector of their partition, not the MBR of the harddisk.
Anyway, Win2k and XP can't be handled this way, so they may use their own start menu in the W98 partition. But I can even modify the BOOT.INI from DOS
BTW, all system backups are made with Norton Ghost 7.5 here. Won't misplace or forget the boot files, won't complain about index.dat dirt, and it can as well run on plain DOS. Images can be compressed, and on FAT32 it splits and joins it's big images automatically.