If the Zotero restoration does not work (hopefully it has worked) then there are other general methods you can try for "forensic data recovery".

But if that is the case you must minimise further usage of your computer since deleted files can be overwritten.

If you need to try forensic data recovery start by clarifying your OS environment .. Windows, Mac or Linux?

For the record I'm referring to the data recovery utilities testdisk and photorec. see http://www.cgsecurity.org

As a precaution against further loss you can also install some Firefox add-ons which hold browser session records .. e.g. Session Manager and Norwell History Tools.

the automated backup, provided it's from the right moment in time, would restore exactly what you had before, including organization.

you will just have one relevant automatic backup. Try that out and either it'll work or not.

I hope that adamsmith's suggestion concerning the Zotero backup works. However, if the auto-backup is a bit too young (after the loss of the organization); do you have an external drive with a system-based backup? Just last week a colleague bemoaned the loss of several hours of work and I knew that he used an automated back up. He didn't think of it in this case. Five minutes later Time Machine restored the files.

Time Machine (Mac) and File History (Win) will do exactly what you need. Each of these built-in utilities (when used with an external drive) can save you. The cost of a large external drive (US$100-$150) may seem like an unneeded expense but when needed it is well worth the cost. My Time Machine backup has saved me from exactly the same problem you have after I worked too fast and cleared some of my Zotero collection structure. It is also good for restoring other lost or damaged files.

If you had lost your database and files, dragonfly's recommendations are sound but are unlikely to work satisfactorily in your case because you changed a file rather than deleted it.

I am making this comment in case you didn't realize you might have been working with a safety net but also to spread the word to others that modern operating systems have this wonderful backup utility that begs to be used.

I tried to do use the automatic backup with no success. Then I realized that my old computer had not connected to the internet in several months and has zotero on it so it is an archive of a 4 month version of my zotero. This is a great discovery!
Now I would like to take its files and put them on my new computer.
1. How can I do that -- with a copy of zotero.sqlite from the old computer transfered to the new computer?
2. Is there a way to NOT lose all the work that I have done over the past 4 months (ie adding new files) on my new computer BUT still get the organization of the documents from the old computer?

Many thanks once again-- I feel so relieved that I have not lost hundreds of hours of work.