I just finished nuking these problems from orbit. Let me explain my progression into darkness and not so far out of it.
MindCrack V8 server. A few custom mod updates and its becoming quite popular, but still small enough that all updates are handled via dropbox. We switch hosts, no big deal, the old host didn't live up to our needs. I learn about MCPC+, which I of course start using build 291. 1 random night I notice some pretty big bugs have been changed in some mods, along with new content, which the users are always happy to see. I update these, and MCPC+ to build 199. I get up the next morning and press start in mcmyadmin, doesn't work, and console is showing errors.
Some googlefu, I find later that any build after 192 and before 201 had this. I upgrade to 202. Then chicken chunks loses its shit entirely, my server starts leaking memory like a sieve. I narrow it down to CC. After downloading the entire server which totaled at 1.5 gigs, I got it working again after much pain & RAM usage to keep the server open long enough to delete the loaders so I could remove CC without another crash, that would break the world.
I upload everything back to the dedicated box and I start it and log on. I died mentally. My entire base, along with my WIP progress base in a MystCraft age where gone. This is not replaceable stuff. I had hundreds of solars and plenty of auto sorting and gregtech stuff, not to mention my entire base took days to make, consisting of 2 volcanos worth of basalt.
I now resolve that nothing short of a earthquake in France combined with 1 in minecraft would make me move hosts or update mods.