Is it true that if you delete a blackberry email account from the handheld it deletes it from the server to your computer like outlook as well? Is there a way to delete it vice versa? How does this work?

If you delete an email from the handheld, it can be deleted on the server at the same time. It may or may not be deleted in Outlook depending on how your email is setup.

It won't delete the account itself, if that's what you're asking.

Is that called email reconcilation?

Yes.