At this point I'm reading this posting and I'm hearing a few things that need clarification...
1. The Skip unresolved option/toggle got toggled on by mistake in Inventor 2017 R2 version release. But if it gets toggled back off under Application Options and you have the proper permission to the registry it should stick. I have not personally seen it where it keeps changing as another user has poitned out.
2. @premysl.misun keeps saying his settings are changing.. Right now I only see one setting in this posting and that's the skip unresolved option. The word settings (plural meaning) to me, means you are experience numerous settings that are not holding. But there's nothing here what those settings are.
3. You said settings are changing when you export to a 3D PDF. What settings are they? Skip unresolved option has nothing to do with export. It only comes into factor when you open your model.
4. You state you have the 3rd highest security. What does that even mean? Are you talking about "Always Notify" on the Windows User Access Control? If so that has nothing to do with settings in Inventor or control or restrict them. That has to do when you install software.
It would just help us if you list all of the settings that you are changing and they are not holding their status. 
Mark Lancaster
& Autodesk Services MarketPlace Provider
Autodesk Inventor Certified Professional & not an Autodesk Employee
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