So I go out for a day last week, come back the next to discover that my entire music library has been wiped.
After much panic and cursing, I find everything intact under "Limewire Files" (shared), but everything downloaded since goes to a new "Saved", therefore I now have to dig through two seperate sources to find a tune and the second isn't available to downloaders.
Any idea why this happened and how I can merge the two again?

No idea at all. You sure someone else hasn't used your computer in the meantime. You have 2 options: 1. Use the original save location: go to Tools>Options>Saving & press the default button & press the apply button. It means you'll need to move your files from the 2nd location to the 1st.
2. Keep the 2nd location. Search for shared on your computer & locate the original files & cut & paste to the new location.

DO a search on your computer for mp3. THis will locate all mp3's on your computer so you can determine what's what & what's where & where any missing ones mighta gone. So once you sort that out .. you can create a folder & put files you wanna share into it .. then go to LW's library window, menu File>Add Folder to Share & direct it to that folder.

By the way I hope you're the admin of your computer & no one else can log in as admin. Thus they can't access your files if you save them to your safe user account area.

If everyone logs in as a separate user then their files should be saved to their own areas ... if you're all logging in as the same user then you're all going to be using the same LW preference settings & save locations & files for sharing.

LOTR:
Thanks & yeah, all three of us have admin. privileges, but it's my Sis & Bro-in-law we're talking about, they don't use this one anyway & we all have our own sides so no biggie.
Never thought about an mp3 search so I will & then let you know.

Regards,
Beetee