Mr. Grun,
First, as suggested by Gunther, I tried the BASEX_JVM environment variable on Windows OS. The dreaded error "Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized" was gone.
After that I installed the BaseX 12.0 beta 7831f9b build, and deleted the BASEX_JVM environment variable. All my XQuery scripts started to work as usual. The error "Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized" is gone.
Overall, it was a such breaking change, a big scare! IMHO, it is much better and cleaner to stay away from the environment variable.
Thanks a lot for such a quick turnaround.
Regards, Yitzhak Khabinsky