There have been many reports recently of missing files and collections. I collected references to a few such reports in a response under  4 days ago (2011-09-21 CET) and the stream of reports has continued since then. The frequency of reports strikes me as unusually high, and so I suspect that there is a new relevant error in the GDocs file system.
The recent reports seem to span all browsers and OS, so I don't think that browser or OS is a relevant factor. I have the impression that more often than normal the reports have something to do with shared files, but some of the reports concern files that are lost to the owner.
Here I want to offer a few problems and related scenarios that are understood and that may explain some instances of missing files or collections. The scenarios that I present here concern only files and collections owned by me. There are other possibilities (many more) for files and collections shared with me.
The problems and scenarios offered here are not new. I doubt that they go far to explain the rash of present reports of missing files.
 Have accessed my documents file and discovered that one document is no longer listed. Can you lose documents?
Hypothetical problem 1. I have lost several files and collections that used to be in my Home area on Google Docs. They were owned by me and not shared. They are not in the trash. They are not found under All items and not in any of my collections and they cannot be found by searching for * under All items.
Variant 1a: I have found one such file in my browser history. I can follow the link from there and then edit it and save it. However, the file is still not found in my file space.
Variant 1b. I have found one such file in my browser history. I can follow the link, but it leads to an error message: Sorry, the page (or document) you have requested does not exist.
Possible scenario: Create a collection L0 and inside L0 create a document doc0. Both are visible in Home. Edit doc0 once or twice to ensure that it is in the browser history. Move L0 to the trash (to bin under UK English). L0 disappears immediately from the Home listing. Wait maybe 10-20 seconds and also doc0 has disappeared from the home listing.
Now look in the trash and find there L0, but not doc0. Look inside L0 in the trash and find that it is empty. Look for files * under Home and under All items, and doc0 will not be found. Find doc0 in the browser history and the behavior is as described; it can be edited, but it does not reappear under Home or under All items after editing.
Once again go to the trash and convince yourself that the trash listing shows only collection L0 and L0 is empty. Then empty the trash. Find now that doc0 is truly gone, also when one follows the link in the browser history.
Resolution: Before emptying the trash search for files * in the trash. Then doc0 will show up.
Of course, doc0 could have been many docs, and collections too.
Underlying this problem is a big error, I think, in Google’s implementation of the user interface. It should be the case that every user item is visible either under All items or in the Trash, and the two locations are mutually exclusive. I think that we understand the (undocumented) procedure of searching for files * to recreate the correct listing if the listing has somehow been messed up. Indeed, looking for files * under All items and then for files * under Trash finds every user item that hasn’t been deleted. Every instance in which searching for files * changes the view reflects an error in the original view. In the case of a collection moved to trash it is an entirely reproducible error that the contents of the collection are not visible in the trash.
I pointed out this error in my initial response (2011-04-11) to the posting  in which it was announced that henceforth deleting a collection would also delete files inside that collection. Later that conversation turned to some much bigger errors in the implementation of that change, namely that it had become possible for people to delete items that they did not own. That truly big error took 2.5 months to be fixed, with most of that time needed in order for the error to be recognized at the Google end of things.
 Trashing a collection now deletes the content too
Hypothetical problem 2. I mistakenly moved a collection and its contents to the trash when I meant to remove only the collection. I restored the content to my documents list, and still my files have disappeared. All items belonged to me and were not shared.
Possible scenario: Same as before; create collection L0 and within it document doc0. Move L0 to trash, so that also doc0 is moved to trash. After the situation has taken hold (10-20 seconds) visit the trash and, having taken note of the previous scenario, search for files * in the trash. File doc0 pops up. Check it and apply “restore to my documents list”. A message pops up saying that doc0 has been restored. Now empty the trash. Find that L0 has been removed and also doc0 has been removed. Alternatively, don’t empty the trash, just wait awhile, and eventually doc0 shows up in the trash listing again. It was always in the trash; only the listing didn’t always show it.
This problem was first noticed here .
 Document kept trying to fight my recovering from trash... and then won.
In connection with the present rather widespread problem of missing files and collections, I wonder if any kind of third-party software is involved.
I recall the conversation early in 2011 on the problem of files getting duplicated 100-fold and worse, and not being able to empty the trash . On that conversation it took 50 contributions over a period of 4 weeks before the following off-hand remark appeared:
"Hmmm, [xxx]'s comment reminds me that many of the files I've uploaded to Google Docs were also likely uploaded using Gladinet. I'd forgotten that.... In case it matters."
It mattered a lot.
So anyone that has a case of missing files or collections to report on the forum can provide added value by reporting also if any third-party software was possibly involved.
 Cannot Empty Trash, Cannot Delete Files