Hello,
I added in Owlready 0.49 some limited methods to control the prefixes.
Here is an example:
from owlready2.driver import _XMLNS
_XMLNS[onto.base_iri] = "my_prefix:"
If you don't have access to the ontology as a Python object, you can directly specify its IRI (with the trailing / or #), e.g.:
_XMLNS["
http://test.org/onto.owl#"] = "my_prefix:"
Jiba