Hi Matt,
There are two separate issues here:
1. Moving the 'ownership' of the app to your company account
2. Changing authentication settings.
For part 1, this is simple: Add the company account as an administrator of
the app, then log in using that account, and remove your personal account as
an
As of now, there is no way to change your authentication setting from
Google Accounts to Google Apps-only, or vice versa, and you can't
delete an application or otherwise re-use the name. It sucks, I'm
currently in the same situation as you.
http://code.google.com/p/googleappengine/issues/detail?