Documents do not simply vanish. Notes is very reliable in that way. You can assume there's some reason for their going away. The most common causes are:

• Someone deleted them.
• The documents are still there but you don't have access to view them.
• The documents are still there but they're not appearing in an expected view because they don't match the selection formula.
• The documents are still there but they're not sorting where you expected, so you can't find them.
• The documents are responses whose main documents don't appear in the view.

Use the "User Detail" button in the second tab of the database properties dialog to see whether any user has been deleting documents recently. Make sure that users don't have access to delete documents unless they have a need to and the training to do it appropriately (and not by accident). In fact, you might want to restrict delete access to your application signing ID, and write agents to delete the documents and log the deletion.

NOTE: User Detail history logging can be turned off; you might have to enable it so that you can catch them next time. This is a clue for why it's a good idea to turn on this feature now, so that when something odd happens, you have evidence about it.

NOTE: Each replica keeps its own User Detail history, so if you see a bunch of deletions coming from another server, open the replica on that server and look at its history to see what user was doing stuff there.

To find whether there are documents whose Reader fields prevent you seeing them, see the Reader And Author Field Troubleshooting links below. Please note that Reader fields will hide documents from you even if you're the database Manager, unless the database is opened in a special administrator mode.

Some things you can do to figure out what's going on:

• The document properties infobox, tab 2 ("i" tab), shows how many documents are in the database, including those you don't have access to.
  
  If there are more documents than you can account for by counting what's in the views, those extras likely are your missing documents, and the problem is access, selection formula, or response hierarchy.
• To see how many documents are in a view, use the Edit/Select All menu, and look at the status bar, which shows how many documents are selected. Note, however, if the view is categorized, a category row counts as a "document" for this purpose, which will throw off the count.
• Use full-text search that will match a particular missing document, instead of just looking where the document is supposed to be in the sort order.
• Create a view containing all documents (SELECT @All) and set the view properties to non-hierarchical (turn off "Show response documents in a hierarchy"). See whether this makes your missing documents reappear. If so, check whether the documents have a $REF item. They might not be visible in other views because of unexpected position, or because their main documents are not also in the view.
• If you can find the document in one view but not another, hold down Ctrl while you open the second view, which makes it jump to the same document in the new view; this is a quick way to see whether it really is there but at an unexpected location.

If the document ends up being in the view but not in the right place in the view, be aware that the response hierarchy affects position, and that sorted columns sort first by datatype, then by value. So if one document contains the number value 56 in a field, and another document contains the string "57", they are not close together in the view, because all the numbers are grouped together, then all the strings (or vice versa, depending whether the sort is ascending).

References

• Tool to analyze whether current user can read/edit a document
• Reader and Author Field Troubleshooting