Migrating from 7.8 to 7.9 Hotfix A. I have engines and search server start

Migrating from 7.8 to 7.9 Hotfix A.
I have engines and search server started properly.
Attempting to start jboss (EAP 6.4) - Getting an error about premature end of file, but it doesn't say exactly which file. Looks like it might be referring to appian-topology.xml. server.log attached
I created the configuration using the configuration using the configure script before I deployed HF A. I see there's an issue addressed in HF A: AN-60118 about invalid default topology being fixed.
Is this the symptom of that? Best way to fix it? I tried creating a new "environment" after the installing hotfix but the generated topology file looks the same.

server.log

OriginalPostID-150670

OriginalPostID-150670