It doesn't affect data model encoded in document even a tiny bit. Namespace prefixes are irrelevant. If changing these prefixes breaks the program, the program is incorrect.
“The C14N-20000119 Canonical XML draft described a method for rewriting namespace prefixes such that two documents having logically equivalent namespace declarations would also have identical namespace prefixes. The goal was to eliminate dependence on the particular namespace prefixes in a document when testing for logical equivalence. However, there now exist a number of contexts in which namespace prefixes can impart information value in an XML document. For example, an XPath expression in an attribute value or element content can reference a namespace prefix. Thus, rewriting the namespace prefixes would damage such a document by changing its meaning (and it cannot be logically equivalent if its meaning has changed).”
