An extension may be interfering. Try disabling them a few at a time and see that way which one is causing the problem.

Scotty2015 said

First time situation occurred folders started to disappear as i read messages TB 31.5.0 win 7 pro 64 bit Thunderbird user forever got into safe mode and disabled all add-ons - now all folders are visible and all content is accessible back to 2009 used mozback so I have backup restarted TB and back to 3 folders. Inbox gets created with the new emails that arrive. Filters send email to one of the visible folders 'Travel' When you open 'travel' all emails 23 unread are accessible. Go back into 'safe' mode and all folders and emails are present Thanks

no extensions , no addons uninstalled thunderbird, deleted all TB folders then rebooted win safe mode and ran Malwarebytes - no malware, rebooted normal windows and downloaded fresh version of TB reloaded profile using mozback. Still the same TB loads showing 3 folders no inbox and should be 2 accounts. Change to safe mode in TB and all files are present and 2 inboxes

  i am not losing data  just can only see emails when in TB safe mode. What TB profile files  could be contaminated?

try deleting panacea.dat

Do you have userChrome.css file in your profile? Are you using hardware acceleration? Those things can influence the behaviour and appearance of the application. http://kb.mozillazine.org/Safe_mode