New mail is going to the wrong INBOX. It is going to an inbox called INBOX_2019 and not to an inbox with INBOX.
I manage my mail into annual folders. I rename the the Inbox to inbox_2018 using standard linex tool down the .thunderbird part. I need to also modify the .msi files. Then I create a new inbox file and its msi file and that makes things manageable. This is working as "normal" but all the new mail is now going to the inbox_2018 folder and it should be going to just the Inbox folder. I notice that both folder have a green down arrow in the leftmost column.
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Really. Thunderbird has an archive system, but you are rolling your own and have issues that it is not working as you would like.
I have never heard of linex tool, and google certainly did not enlighten me, but based on the existence of a folder with archives.sdb.unknown in the name, I would guess your profile is actually something of a mess. There is now a replacement archives folder and all your archives appear to be in this mangled folder.
I would think failure is not all that far from a reality. You appear to have been relying on Thunderbird's ability to ignore missing files and just recreate them as needed. That is hardly a good approach, but perhaps workable if managed very carefully.
Just at a guess the account directory in account settings has become mangled. Possibly for moving something while the program was still executing. But really I am not sure where you go to restore your profile to an ordered condition where I would trust it.