Sometimes Mozilla Thunderbird does not show messages and this could be due to the corrupt folder index (.msf) file. You can fix the damaged or corrupt folder index by using the repair option.
Right click on the folder which does not show the messages, and select Properties from the menu list.
This would display the following Folder Properties dialog box
To repair the folder, click the Repair Folder button available as part of the Folder Properties dialog box. This might fix the missing messages or deleted messages continue showing problems.