Where are the libraries that you are referencing?
In 3.1.1 and prior, if you copy a file into "domains/<domainname>/lib"
or any subdirectory of that directory, an instance has to be restarted
in order to get the library sync'd. And, if no change has been made to
domain.xml, a full sync is required, i.e., --sync=full on the
start-instance command.
Tom