ync_emergo Try to reproduce the problem in a fresh project.
Scene changes + saving resets after restarting Godot to old values
ync_emergo I can't really make my scene lokal because I want it to keep the inheritance in case I have changes to the .blend file.
but then you want make changes in the mesh position in the scene??
My brain cant wrap around too many words... maybe make a video? demonstrating whats going on? You can use streamable to upload videos or other services.. idk...
Maybe you moved something and forgot about..
the issue is not even reproducable in the same project. I have the same scene structure with several scenes that inherit from a blend file and the issue only appears for one scene.
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video showcase:
explanation for the video:
The scene "seat_1" is used in the scene "seat_1_prefab" as one of the child nodes of its root. As seen in the video, the default position and rotation of the "mesh_container" node differ in both scenes, although they originate from the same scene. As shown, when I change another value, e.g. the scale of the transform, it is adjusted in both scenes accordingly and at the same time. only the values for rotation and position differ.
Precice explanation of the bug (i think it is one) in my earlier posts here.
ync_emergo Is it reproducible with that exact scene?
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- Duplicate the project
- Duplicate the blender file
- Remove everything except offending node from the blender file
- Export
- Remove everything except two offending scenes from the project
- If the cause of the problem hasn't become apparent - post the project
I changed this to the help tags. 
Unfortunately I cannot share the entire project here. I tried to create a new project and copy the corresponding scene and blend files over to the new project, however I was not able to reproduce the issue in the new project.
For now, we're just using a work around. Thanks for your help 
ync_emergo Unfortunately I cannot share the entire project here.
If you strip it down to contain only the problem, why not?
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I actually found the issue now. The animation player somehow resets my position automatically on scene load. If i disable the animation player or remove it, the issue stops.
I made another video for an easier visual representation of the issue:
I'm not familiar enough with animation players to tell if this is intended or a bug, however it is certainly very confusing, imo.
ync_emergo Animation player is probably trying to animate that property.