mail considered "junk" is being permanently deleting, not going into junk folder for review
After I updated Thunderbird a couple of months ago, I noticed that there were no longer any items in my junk mail folder. Then I noticed that while I was downloading my mail into my inbox, I would very briefly see an email coming in that would suddenly disappear. This didn't happen to all mail; it happened periodically. I tested by sending myself an email. I saw it downloading into my inbox briefly then it was deleted. I think this must be a problem with Thunderbird thinking mail is junk, but instead of sending it to the junk folder, it gets erased. I do not have any anti-spam or anti-virus software running on my Mac (unless something came already installed that I'm not aware of).
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Look in your 'Trash' for those missing 'junk' messages. If you find them there, you did not tell Thunderbird to place them in a 'Junk' folder.
Set up a junk mail folder Thunderbird Menu Bar Tools - Account Settings - select accountname - Junk Settings
In the section Destination and Retention tick 'Move new junk messages to: ' select 'Junk' folder on: 'you choose - I suggest local folders?'
Also notice the tick box for 'Automatically delete ...' - with a window to enter the number of days before they are deleted. Choose a small number 7 to 14 is fine. They will be removed from the junk folder after this length of time and will be put into the trash. Do this for each of your accounts. They can all share the same 'Junk' folder on local folders.
TB-38.3 Win10-PC