From what I heard at the Elevate keynote presentation, Appeon has reversed the decision to eliminate PBL files - they will be around for the foreseeable future. As Chris mentioned, PB 2017 R2 will natively support GitHub and SVN.
I personally use Plastic SCM. It has a unique graphical interface and an intuitive approach to branching and merging. Plastic provides an SCC-compatible plug-in, which is needed to work with PowerBuilder, but causes issues from time to time, usually related to the PBG files (another reason to get rid of the PBL). I'd recommend at least checking it out: plasticscm.com