Never tried it, but lilo is a boot manager, not a partition mutilator (tho experiences vary). When im doin stuff on partitions Id like to use Partition Magic. It may be expensive to buy, but its damn reliable. Never failed me.
I think tho u dont wanna remap partitions each time u boot, it aint a software thing & HD's wherent built for that kinda toyin around. I think u better rethink ure partitioning strategies:
would be a better division, cuz now all apps reside on one disk, reachable for each OS.
If this is too much hassle, Partition Magic will allow u (to some extent) to hide & unhide partitions an OS may see on boot.