Does sharepoint try to resolve conflicts as it crawls through its
databases?

We have a situation where we changed the site definition for our
team room teamplate on Tuesday. 2 days later, the libraries that we
were trying to change by modifying the site definition became
corrupted. The error we get when publishing files is "Form
validation error. The URL 'Libary name/file name.doc' is invalid. It
may refer to a nonexistent file or folder, or refer to a valid file
or folder that is not in the current Web.

We get a similar error when trying to modify properties on a file in
the library. Another interesting thing. Even with this error, the
files does load to the library. While you cannot see it in the All
Documents view or any view you create through the GUI, you can see
the file in the library when you use the Explorer view or view the
library from My NetworkPlaces. Some how, the aspx pages have become
corrupted, and we cannot figure out how it happened, nor why it took
a couple of days to appear.

Has any one run into a problem like this or found that changes have
unexpected outcomes that are not created immediately?

We are worried that if we create all new libraries and move the
files to them, the server could recorrupt the libraries again. Any
thoughts would be appreciated. I am also concerned if we delete
libraries and recreate with the same name, the server could think
the new libraries were missed during the initial deletion and delete
them again.