What is your anti-virus software?

To avoid problems with anti-virus software it is recommended to create an exception in your anti-virus software for the Thunderbird profile folder, so that the anti-virus real-time scanner will not scan it. https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data#w_how-to-find-your-profile

I have AVAST antivirus but I never had problems like this from at least 10 years. But anyway even after inserting the exception, how do I stop all the old emails from being downloaded again? I read that to download new emails, thunderbird uses the popstate.dat file ... is there a way to modify that perhaps?

I read that to download new emails, thunderbird uses the popstate.dat file

Correct, however, the popstate.dat file may be corrupt in your case. You can try to delete popstate.dat to fix it. See https://kb.mozillazine.org/Popstate.dat

Having said that, accumulating a large no. of messages in Inbox is asking for trouble. It is best practice to keep Inbox as tidy as possible. https://kb.mozillazine.org/Keep_it_working_-_Thunderbird

Based on your description it sounds like in Thunderbird's Server setting you have enabled "leave messages on server". Enabled is not the default setting for this option. Enabled is not a great choice. And if you have it set, you MUST manually manage the messages on the server so that you don't accumulate thousands of messages.

If you delete popstate.dat it will most certainly download every message currently the server. Creating your own popstate.dat is not easy. Frankly, you might be better off creating a new account in Thunderbird to access this email address with imap rather than pop.

Is it not possible to modify the popstate.dat file to make thunderbird "believe" that it has downloaded emails up to today? I really don't want to have to download 15,000 emails again! :(

Today thunderbird crashed when closing... and I still haven't solved my problem. What do you suggest I do? Is it not possible to modify the popstate.dat file to make Thunderbird believe it has downloaded all the mail up to today?

As far as I can see the only way I have is to re-download all the mail from my email inbox (over 15,000 email!).

How can I have all the mail in my account downloaded again to another folder instead of the "inbox" folder where I currently have all the email archive? I was thinking of having it downloaded to another folder so I can then delete it and only have emails downloaded from today onwards to my "inbox" folder.