TB doesn't support folders on removable media, but you can copy the actual files for a certain folder to a removable medium. Afterwards delete the contents of that folder in TB
(not the folder itself, that would complicate the restoring process) and when you want to search your archive you copy the files for that folder back to their original location and TB can search that folder. (I'd close TB when restoring the files, even though I'm not sure whether it's really necessary.)
This way of restoring folders ony works for the full folder, not for a partial restore.
Keep in mind that your backups cannot be used again after you've done a major upgrade to 5.0 or 5.1, so before upgrading you should restore the folders and after upgrading you should create new copies on removable media.

For the rest, I'd suggest that you sort you archive folder into multiple archive folders, each for a year or two.
It's not that TB has a limit of 35000 messages per folder, but you're mentioning corrupted data, so it's best to tackle that problem.
Create a new folder, copy a bunch of messages to it and archive it. Do this for every two years or 10000 messages, whatever's convenient.
I mention that you copy them from your archive folder instead of moving them. That's because moving them from your corrupted folder might create more damage to it, as it's altered. While copying from it doesn't alter it. After you've copied all messages from your archive folder you should check whether the new archives are ok (with the maintenance centre) and then you can delete your old archive.

In the first part of my message I told you to copy the files for the archive folders.
TB stores all of its files in the Mail Directory.
That Mail Directory contains a directory for every account you've got, each account directory contains directories for the folders of that account (unless it's an imap account), all nested folders have their matching directory nested in the directory matching their parent folder. (Unless you're using an encrypted message base, pro version only.) Account directories have the same name as the account is named in your account tree pane. The other directories have the same name as their matching mail folder. (Unless you're using an encrypted message base.)
In case you're using common folders, their matching directories can be found in the mail directory. (Same level as the account directories.)
The default location for the mail directory (for current versions of TB) is %userdata%/The Bat!
That can be overridden during install, you can find the actual location of the mail directory via:
Options -> Preferences -> System -> Mail Directory

I hope this helps