The disclaimers for changing a site  Definition (especially those with
existing Sites) are stronger than those that are often given when changes to
the registry are suggested.

Not sure what actually happened  but the following warnings can be found  in
the SDK:

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Warning Making changes to an originally installed ONET.XML file  on a server
running Windows SharePoint Services can break existing sites and the changes
may be lost when Windows SharePoint Services is updated such as through
service packs or patches. Whenever possible, create  a new site or list
definition as opposed to modifying  original schema files. For more
information on the best practice to follow, see Creating a Site Definition
from an Existing Site Definition.
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Warning It is recommended that you create a new site definition  rather than
modify an originally installed site definition:
* Use of repairs and service packs could revert your modifications.
* Custom templates based on the original site definitions may not work.
* Site definitions with references to original list definitions may not
work.
-------------------------------------

Making changes to a Site Definition after content exists is very risky,
especially if something has been unghosted. Additions are typically OK, but
there is always a risk when making changes that something could go awry.