I rarely use the OOPS window, so it could rearrange itself every save and load for all I know, :). I do find it handy to track down references and such occasionally. Although, I think I tried to use it more often when I first started using blender and spent a bunch of time organizing it only to loose my work. This might be why I don’t use it much any more, that and organizing stuff into layers helps me find things pretty quick anyway.
I know most of the things I run into that would fall under what you call file corruption, generally have either one of two causes when I experience them. One of these is just running into a blender limitation or minor misfeature (not really a bug, but not the way you want something to work). I’d be tempted to say that your issue with the OOPS window falls into this category.
The other normal cause of problems like this for me is either not really understanding how something in blender works or making a change to something and leaving something old in place or not fully propogating the change. This is especially true for me when working with armatures since mine are very much a WIP much of the time. I just keep trying to squeeze that last bit of automation into them, :).
If you’re having problems with armatures, make sure you check them for old constraints that should be removed and also insure that any new constraints or parenting changes have been fully propogated. Having NLA action strips on an armature and/or having an action assigned in the action window to an armature can produce very unexpected results sometimes.
Also, with armatures, somtimes I get a bone rotated or moved and when I switch to another action, the rotation or movement isn’t reset. When I see a problem with an action that used to work, one of the first things I do is AKEY to select all the bones and then ALT-GKEY, ALT-RKEY and ALT-SKEY to reset position, rotation and size. Then arrow one frame forward and back to test again.
Not sure about the eyelash problem as you didn’t really describe it. You may want to look at getting a CVS build though as blender has been going through massive changes since 2.28 and I’ve run into more bugs with the 2.3x releases than normal. I expect this will settle down soon, say another official release or two, but its possible you may have run into a bug that’s been fixed in CVS already.
Beware though that while most CVS builds improve upon blender, there are bugs and other issues you might run into because its a work in progress. Wait for official releases if you are risk adverse.
To help me minimize loss of work, I have autosave enabled and have blender keep five versions of my file. If I’m going to do something dramatic and potentially destructive, I make sure I save my file right before I start the changes and will generally make an additionaly temporary copy of that file with a name to remind me why I did it. Then I delete those files after I’ve completed my major change and am satisfied that it works. Additionally I backup my .blend file and its numbered backups once a day into an archive. Since I’m not running tight on disk space atm, these have accumulated over the last few months and I can retrieve five versions of my project from any of those days. Yeah, overkill, and I rarely need them, but I’ll delete them if I start getting tight on disk space.
Alternatively, I’m looking at being able to use CVS or other more binary friendly version control system. But I think this whole issue deserves its own discussion, which is the reason I came to elysiun right now. Look for another post from me soon.