I vote to have an option e.g. in config "Save layer status with the model" set as default to yes!
This is easy to solve by a mapkey for saving the model, but non-experience user can be really surprised next day if open the model from last day.
For meself I know if we save the model from the drawing and previously we hide some elements within drawing enviroment then without separate save status you can be also surprised...
I would support the idea of adding a option but not setting the default to yes. This would be a major functionality change that would cause endless modifications to parts and assemblies that have not actually changed other than layer status. When working with assemblies, especially large assemblies, a simple layer change in the assembly could potentially modify every part in the assembly. This would not be acceptable behavior as default.
I can't tell how many times I use auto-check-in function and face-palm as I see the message "Warning! Layer status not saved" shows up in the status bar.
But I agree with Stephen, automatically saving layer status with the part should not be defaulted to "yes".
I submit that there should be an option to turn the warning message into a prompt that the user would have to answer:
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