Maybe this will help - I have two snapshots of my workspace, the first is my current changeset, the other is from an old branch that is basically an old maintenance version of the app that gets occasional maintenance updates. In the current version, the link to jpatools is at changeset 40, the old version it's at 2. That's all as expected. However, when it's displaying changeset 2, I check the actual tools directory and the files are still dated this month and have the most recent changes, which is obviously a problem for a build expecting 2017 files. I hit "update workspace"
I guess I don't see a lot of difference as my workspaces seem to be local copies of repositories, but hopefully this gives a clearer picture.