I am trying to transfer my gmail messages to Thunderbird. I have around 5000 messages, but they seem to stop accumulating in the inbox after 3000 messages. So I have moved the older messages to a new folder in Thunderbird. But I am worried now what will happen when Thunderbird synchronises with my Gmail account. Will the messages still be there? Will they keep their labels?

Is there any way to ensure my messages are kept intact.....?