Please see this issue,
protegeproject/swrlapi#25
I am facing a similar issue where i have to use an object_property (let's assume hasQuality) of an imported ontology, but when I try to execute rule, People(?p),hasQuality(?p,?q)->Patient(?p) I get the error ValueError: Cannot find entity 'hasQuality'!. Note that People and Patient are in the main owl file, which imports another owl file which has the property hasQuality.
Thank you in advance.