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If you're trying to import them from Thunderbird into Gmail webmail I'd expect you to use a IMAP account and either drag and drop the messages or use copy/move commands. You can't upload messages via a POP account. I'm wondering if you accidentally created a POP account instead and unchecked the "leave message on server" setting in the accounts server settings or something like that.
If you move the messages you want to upload to the "Local Folders" pseudo account in Thunderbird they will be safe from any side effects of your POP or IMAP accounts. That is the main reason why 'Local Folders" exists. Then copy the messages to the IMAP account.
Or try creating a child folder (in the IMAP account) and copying the messages to it, rather than the inbox. You could then log into Gmail webmail afterwards using a browser and move the messages to the inbox. You shouldn't have to do that but its quicker than trying to troubleshoot what caused your problem.
Keep in mind that Gmail has a undocumented hourly and daily bandwidth limit for email clients. If you have lots of messages (especially ones with large attachments) you might have to do the upload in several steps, over time.
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