I believe I've found a solution for building 3.9.x using the parent pom 3.6 settings despite the fact that it's sourcing from 3.10 version (in master) for some of the projects.
This should allow us to build 3.9.x without branching the remaining projects. As long as this workaround works for another month or so (through Oxygen.3a) we'll be done with the 3.9.x stream.
Workaround is simple: override the property values in parent pom 3.10 with the values from parent pom 3.6, as per the job config here:
tycho.version=0.21.0
tycho-extras.version=0.21.0
license-repo.url="" href="http://download.eclipse.org/cbi/updates/license">http://download.eclipse.org/cbi/updates/license
gef-repo.url="" href="http://download.eclipse.org/tools/gef/updates/legacy/integration/">http://download.eclipse.org/tools/gef/updates/legacy/integration/
platform-repo.url="" href="http://download.eclipse.org/eclipse/updates/4.7-M-builds/M-4.7.3RC2-201802150545/">http://download.eclipse.org/eclipse/updates/4.7-M-builds/M-4.7.3RC2-201802150545/
orbit-repo.url="" href="http://download.eclipse.org/tools/orbit/downloads/drops/M20180206163158/repository/">http://download.eclipse.org/tools/orbit/downloads/drops/M20180206163158/repository/
jetty-repo.url="" href="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.7.v20170914/">http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.7.v20170914/
emf-repo.url="" href="http://download.eclipse.org/modeling/emf/emf/updates/2.13milestones/">http://download.eclipse.org/modeling/emf/emf/updates/2.13milestones/
jgit-repo.url="" href="http://download.eclipse.org/egit/updates">http://download.eclipse.org/egit/updates
dtp-repo.url="" href="http://download.eclipse.org/datatools/1.14.1.201712071719/repository/">http://download.eclipse.org/datatools/1.14.1.201712071719/repository/
emf-transaction-repo.url="" href="http://download.eclipse.org/modeling/emf/transaction/updates/releases/">http://download.eclipse.org/modeling/emf/transaction/updates/releases/
emf-validation-repo.url="" href="http://download.eclipse.org/modeling/emf/validation/updates/releases/">http://download.eclipse.org/modeling/emf/validation/updates/releases/
graphiti-repo.url="" href="http://download.eclipse.org/graphiti/updates/milestones">http://download.eclipse.org/graphiti/updates/milestones
eclipselink-repo.url="" href="http://build.eclipse.org/webtools/downloadsites/eclipseLink/eclipseLink-2.6.0/">http://build.eclipse.org/webtools/downloadsites/eclipseLink/eclipseLink-2.6.0/
swtbot-repo.url="" href="http://download.eclipse.org/technology/swtbot/releases/latest">http://download.eclipse.org/technology/swtbot/releases/latest
webtools-common-site=${platform-repo.url}
webtools-servertools-site=${platform-repo.url}
webtools-jsdt-site=${platform-repo.url}
webtools-sourceediting-site=${platform-repo.url}
webtools-jeetools-site=${platform-repo.url}
webtools-dali-site=${platform-repo.url}
webtools-jsf-site=${platform-repo.url}
webtools-webservices-site=${platform-repo.url}
skipITests=false