Messages have disappeared from my inbox.
I tried to Repair the folder and have deleted the Inbox.msf file without success.
The .msf file is 44kb although there were 4500 messages in the inbox.
Is there something else I can try?
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What is the size of the Inbox file? If it's greater than 0 bytes you can try to open it with a decent text editor and check whether your messages still exist.
Beyond that you can restore your messages from a recent backup of your Thunderbird profile, assuming you did create one in the first place.
In general, it isn't best practice to accumulate messages in Inbox, as Inbox is most susceptible to corruption. Corruption is most likely caused by anti-virus software messing with Thunderbird mail files.
It is therefore recommended to create an exception for the Thunderbird profile folder, so that the real-time scanner won't attempt to scan the profile with your mail.
For more information on the profile location see http://kb.mozillazine.org/Profile_folder_-_Thunderbird
Also see http://kb.mozillazine.org/Keep_it_working_-_Thunderbird