I guess with some work you could get them all there to TB.
I don't use Hotmail, so the first thing I would try if I could was move messages from the folder to the inbox. If you can do that, it would then be easy. If you can NOT do that, the next thing I'd try is forwarding all the messages in the folder to yourself. Once in the inbox of course you could then get it to TB.
In TB I'd create similar folders and rules to automatically move the messages there. Then run the rule once all were in. Of course this might not work as well as it should if you can't move the Hotmail messages in folders into the inbox. Normally I use the FROM: to determine which folder incoming messages should go to. Once I get the e-mail in and TB puts something into a folder it shows that new messages are in the folder and I look in the folder. With the above method you'll need to do a different type of rule looking for specific data maybe. Either that or once you get the mail in, you, via the RMB on the message, MOVE it to a desired TB folder.