I made the switch from 6.8.0 to 6.9.1, so I can give you a little "heads up".
1) check out official branch.
2) delete everything.
3) extract occt official tarball
4) run script/commands to clean the repo. This is in the log of the official branch.
5) make commit and tag.
From here you have a choice of whether to use a git workflow or a patch workflow. denis started updating the patches for 6.9.0, but I don't think he finished. I never updated the patches for 6.9.1. So the 691patched_3 branch, that has the changes contained in the patches, is a little more current. I guess I will stop here as everything that follows will be dependent on your workflow. Does that answer your questions? You can view the schooling Denis gave us before the 6.9.1 update. https://gitter.im/tpaviot/oce
IMHO: I think the repo organization and workflow is poor. A better process will make updating to occt releases .... less hard. Here is what I suggest: The master branch should be an exact mirror of the occt master branch. Each official occt release should be applied from a diff to the master branch. All oce work is done in branches off master. No merges into master. The first commits of an oce release branch can be the results of the script/commands. As oce changes come in, they get applied to the current release oce branch. Then when it comes time to do an occt official update we have a more natural rebase --onto situation. The fact that the oce repo is not a remote to the occt repo, makes a typical merge workflow poor. Extra effort needs to be made to keep the oce changes completely separated from the occt code.