create a new folder named 2006 or something. Move there the old messages, if needed create subfolders - you can do this either manually or with filters, using TimeOf as a condition.

Then just delete the new folder.
TheBat will ask you how - select to 'leave message base..' - this way nothing will be lost, just TB will not load this folder at startup, will not search in it when you search etc.

If you need the old ones, press CTRL+ALT+SHIFT+L , which will force TB to read all folders under the account dir. Or create a new folder with the same name. When you finish, just delete the folder again the same way.

Yes - use XCOPY. It will recreate a directory structure with or wothout files wherever you wish
You can open a command window at the bats folders and reproduce the entire structur

Start with XCOPY /? to get the commands and switches

Personally, I use an outside utility to  copy the emails into an archive area then RAR them - then totally delete them from the bat

The whole rebuilding process isn't entirely automatic and the copying stuff has to be done with a little understanding, but then you can get rather far with it.
Suppose you've got an account called Michael with lots of folders and full with messages of 2006 that you want to archive.
You go to your mail directory and create a subdirectory 2006 and you copy the full contents of your Michael account (that's the same as the Michael subdirectory in the mail directory) to 2006.
Next year when you want to search something back, you just say to TB to create a new account and call it '2006' and TB will say it knows that and come back with the settings for your Michael account as those were copied to the 2006 subdirectory. These identical settings are something you've got to realise so the first thing you do is to change the transport settings of the 2006 account in order to prevent it from downloading your 2007 (or later) messages into your archive. When you're done with your archive search you delete the account again (but leave the account files on disk) and you're done.

When you merely want to copy the folder structure to a new account let's call it 2007, first you create an account with TB, close TB afterwards.
Start a coomand prompt window, go to your mail directory and type 'xcopy michael 2007 /t /e' next you copy the file 'account.flb' from the michael account to 2007, when you're running OTFE (encrypted message base) you need to copy account.efb too.
The account.flb file stores the folder structure, but not only how the folder are structured, but also folder properties.
In caae the folder structure isn't the only thing you want, but you want the filters to be copied too, then you copy the account.srb file too (account.erb for OTFE)
Take care that copying account.* files to account directories needs to be done with TB shut down, to prevent unanticipated problems.
Other usefull files are account.cfn (account.efn for OTFE) with the account properties and account.qtn (account.etn for OTFE) with your quick templates.

So you can copy whatever you want as long as you keep the stuff above in mind.

Copying an folder structure into another account with an existing folder structure that doesn't match, means that you can't copy the account.flb file as that would overwrite the previously existing file. For this TB has an additional trick.
Start TB, set focus on a folder in the account tree pane and press Ctrl-Alt-Shift-L, this hotkey will search for lost folders and those to your TB folder structure.

Well another option would be some third party archiver for email, ever heard of Mailbag assistant?
http://www.fookes.com/mailbag/
It's rumoured to be quite good.