EnterprisePharo is on master and there have been few LaTeX-level changes recently. The parent commit of master dates from april when we migrated a few books, and the recent commit was documentation.
I think at a minimum you'll have to use a different latex exporter in the pillar.conf (check EnterprisePharo for that) to output the sbabook-specific environments and macros, but if there are problems beyond that it's a matter of how the main file and the templates are combined. At this point my recommendation would be to migrate to the makefile-centric build of EnterprisePharo. I've just tried to build PBE but the VM that ./download.sh gets crashes���