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The OpenStudio SketchUp Plugin and the stand alone OpenStudio application have always dealt with thermostats in a different way, which is confusing, and is something that we do need to address. In the underlying API a Thermostat is a shared resource that can be assigned to more than one thermal zone. It is accessible in the plugin via the inspector and also the space attributes dialog. The thermostat object is really a holder for a two schedules; a cooling and heating setpoint schedule.

In the stand alone OpenStudio application the user is shielded from seeing the thermostat object. Only the two setpoint schedules are exposed. Under the hood the approach is more like the thermostat is a child of a thermal zone and when starting from a clean model the thermostats are created when you drop schedules onto the setupoint dropzones.

Generally either of these approaches are fine, but the issues occur when you start in the SketchUp plugin and assign the thermostat to more than one thermal zone. Then you move to the OpenStudio application and try to change the thermostats for just one of the thermal zones. If you change one, they all change, and you can't detach them from each other.

In just doing some testing now I have confirmed a few things.

1. At first glance when you do add a thermostat to one zone, it looks like it only affects that zone. But if you leave the zone tab and go back, or if you inspect the file you will see it did change all of the zones using that shared thermostat.
2. With the removal of the on/off button for thermostats, which was generally a good thing, an un-expected byproduct is that you can no longer detach the shared thermostat from within the OpenStudio application. When you remove both the heating and cooling set points, the thermostat is still there, vs. mimicking what the off button would have done in the past.

There is an open issue for this, I'll update it with this information, which reflects change that came in with grid view thermal zone view. Thanks for providing the detail about what was happening. For now you will have to jump into the Plugin like @TaylorRoberts suggested.