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Just hiding and saving won't work as you write since that is thought to help you during edit only not permanently hiding.
There are 2 ways to keep polygons hidden I know:
1. Way:
Step 1: If the polygons you want to hide aren't assigned to a surface group yet mark them with geometry editor enabled.
Step 2: Create new surface group (right click -> "Geometry assignment" -> "Create surface from selected" -> name it.
Step 3: Switch to surfaces tab, mark your created surface and search for "Cutout opacity". Then put the slider to 0 if you want to make them full invisible. Save your project and they will be kept hidden.
2.Way: For rigged objects you can hide / unhide geometry with hiding their bones (scene tab). That will be saved aswell.
