One of the reasons that people choose to use Git is how easy it is to do branching. Unfortunately, PowerBuilder hasn't implemented it yet. But that doesn't stop you from using this feature if you don't mind taking a few extra steps.
Suppose you are working on the master branch and now need to to work on the dev branch
1. Close PowerBuilder.
2. Stash your changes in master branch using TortoiseGit.
3. Switch/Checkout the dev branch.
4. You can double click on the pbw file to start PowerBuilder. Make sure you click Refresh to get all objects from the dev into the IDE.
5. You can do your development in the IDE and you can also use the Git Commit in the IDE to commit to dev branch.
6. When you are ready to submit your commits in dev, you can use TorotiseGit to push it to the server.
7. You can switch back to the master branch using the same method mentioned above.
8. Use Stash Pop (if you need to apply the last stash) or Stash List > Stash Apply to restore the previous status of your master branch.
9. Restart you PB and do a Refresh then you can work on the master branch again.
Now it's clear to me
I found that using the Add to Source Control function does not take account of the existing status of source controlled items. Even if they have been modified locally, all the source is represented as being in sync with the server. For anything in-flight, that will lead to a host of problems.
So neither method addresses the use case of hooking up a new installation of Powerbuilder, even just upgrades, with existing source controlled folders. But I found a workaround for this. After closing Powerbuilder, I renamed the source folder I wanted to hook up to a different name, suppose it was named "source" I renamed it "source_backup". Then I created a new folder named "source", and used "Connect to Workspace" to download the current master to it. Then after closing Powerbuilder again, I discarded the "source" folder and renamed "source_backup" to "source". Similar to the accommodation of branches above, Powerbuilder now shows the folder as being source controlled.