Replace these popups by something that does not have to be acknowledged by the user.
e.g. status light or progress bar in DPL’s toolbar. Maybe the progress icon could be reused with a tooltip pointing out the action that triggered the progress bar.
When I manually export or import DOP sidecar files, the popups appear.
If automatic import/export is active, the popups do not appear. If not showing the popups is okay with automatic import/export, it might as well be okay that they stay away when automatic i/e is off.