I'd hazard two guesses
1) the inbox is corrupted and needs repair using the inbox repair tool
How to use Inbox Repair tool to repair pst file in Outlook
2) your outlook PST file is in a nonstandard location, and for some reason Outlook has reverted to a standard location, orphaning the file and creating a new inbox. To repair it try system restore, or else manually editing the data file store locations with the account settings