We actually don't track PBLs in our Git repo at all. We use an orca script to build brand new PBLs from scratch when doing a new build. It's worked really well. We do something similar to this:
git fetch --all
git reset --hard origin/master
That will pull the latest source from our repo and wipe out any trash left behind from a previous build.
Then we have an orca script similar to this to generate new PBLs and then deploy new PBDs and a new EXE.
start session
scc set connect property localprojpath ".\"
scc set connect property logfile "C:\buildserver\root\logs\build.log"
scc set connect property logappend false
scc set connect property deletetempfiles "true"
scc connect offline
scc set target ".\example.pbt" "refresh_all importonly"
scc refresh target full
build library ".\example.pbl" "" pbd
build executable ".\example.exe" ".\resources\example.ico" "" "y" newvstylecontrols
scc close
end session
