I code with Processing for years (on Windows) and I never had this issue. Perhaps you should indicate what is your platform.

Another point I cannot stress enough: use a source code control system (or VCS: version control system). It can be SVN if you are familiar with it, or the more modern Bazaar, Mercurial or Git (DVCS, D is for distributed).
I have the files on my local disk, and I can synchronize them on various computers or USB keys, and I host them in Launchpad (free), to share them with others or just to facilitate synchronizing.

And, of course, regular backup is also a good thing...

Of course, these are general advices, it would be better to have a good editor! The PDE is a good environment but an awful, dated editor.
SciTE isn't really an option, I believe the MacOS version isn't on par with the others (but the main developer wants to make a payware version for Mac).
I believe that the Processing developers wanted to use the Eclipse (or NetBeans?) core/framework to make a good editor with debugging capabilities. I don't know if the project is ongoing.
Well, for serious editing work, I use SciTE and reload the project in the PDE to run it...

I'm on Ubuntu/Mint. Sure I would have used version control, it was just an experimental sketch. Stupid really, although wiping the whole file not what you expect. If the file had been deleted I might have been able to recover it. However it was overwritten with nothing. Chances of recovering not 100%.

They might not be able to use Scite for mac, but there is usable code they, especially the SCIntilla core.

I don't have a problem with Eclipse, although maybe a bit heavy weight for some applications like teaching.

Is Geany any good?

geany's ok. give it a try (it's free after all, all you have to lose is 2MB of diskspace)

i am dyed-in-the-wool vim user but vim's terrible for writing java code where you're often editing multiple files in deep trees at the same time (not so much when writing processing sketches, but work-related projects). geany, with it's file tree on the left, was much better for this. it does java highlighting. and you can assign actions to the Make task (and menu button / funciton key) to, say, restart processing with the newly-edited file opened.

or go the whole hog and jump to eclipse with it's method completion etc.

have to reiterate what phi-lho said though about using svn or git and decent backups*. a sketch you've been working on 'for months' is worth keeping track of. (i've also never seen it happen, but that doesn't mean it doesn't)

* i use an external disk and dirvish, which is in ubuntu repositories and does what timevault does. incremental backups, no trouble.