I am assuming your question is with regards to the PegaApp classloader OR how PRPC would prioritize and load a duplicate class existing in multiple JARs from the PRPC database table.
PRPC ClassLoader would prioritize any duplicate class in the following order -
1. Latest "PZPATCHDATE" in case there are multiple classes with the same custom "PZCODETVERSION" and "PZCODESET" (non 'Pega-Enginecode').
2. If there are no duplicate classes in custom "PZCODETVERSION" and "PZCODESET" (non 'Pega-Enginecode'), PRPC will then look within 'Pega-Enginecode' "PZCODESET" and "PZCODESETVERSION" to try and load the class.
Any JAR that you upload via "Application > Distribution > Import" wizard by default will have a custom codeset and codesetversion, so will always get precedence during Class loading from any duplicate class present in "pega-enginecode" codeset and codesetversion.