Where do you keep your messages? All lumped together in your Inbox?

Zenos said

Where do you keep your messages? All lumped together in your Inbox?

Yes I do... all in my Inbox

Your mail provider may have a policy or may have recently enabled a policy to automatically remove old messages. If this is doing the damage, the answer may be to file the messages in other folders.

Thunderbird does have settings for disk space which can delete messages when they reach a certain age. We can't discount the notion that such a setting may have become enabled, perhaps after an update.

Tools|Account Settings

Select the account.

Look for options that mention Disk Space or Synchronisation & Storage for settings related to management of messages according to age or size, and make sure none of these are causing your problem.