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OpenStudio only imports geometry, constructions, loads, thermal zones, and schedules , so if you export an IDF and modify it, when you re-import it, you'll lose everything that isn't listed above (even things that were originally added with OpenStudio).

If you need to make changes to your model that OpenStudio does not yet support and you still want to be able to use the OpenStudio Application or PAT, I suggest using an EnergyPlus Measure to make these changes. With an EnergyPlus Measure, you can add/change/modify anything in the IDF.