Hello Ray best,
To solve the issue of disappearing outlook inbox files we first need to diagnose what could be the possible source of this mishap.
Case I
Add ons : Add ons cause hell lot of issues in MS Outlook functioning.Try to uninstall them or remove the buggy ones.Below are the steps for removing Add ons-
1.Goto Run(type Run in the start menu and select it/press Window+R button)
2.Type Outlook/safe .This opens the outlook in the safe mode and then try to disable add ins.Here's how you disable add-ins :
File->Options
select Add-ins->select COM Add – ins
under Manage ->Click go
Select all the addins to disable and click ok.
Case II
Manually select the root folder path
FILE - Account Settings - Account Settings - Change - More Settings - Advanced

Where it says Folders - Root folder path:
Enter: inbox

Feel free to ask queries for further issues
~Dex