Your Inbox in your mail file has become corrupt for whatever reason. Because the Inbox is a folder, it does not use selection formulas to give a collection of documents. It is built by the router depositing messages there. Once the folder is destroyed or replaced, the collection is lost with it. After replacing it with a new one, only new documents will be deposited in it from that point on.
Below is a script that can be used to repopulate your Inbox with the older mail messages that have not been currently filed in folders. The script can be placed in a button and mailed to the users who need it.