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Do you work with external reference (XREF)? You probably found this issue. You turn off or freeze layers, save and close the file. When you open the file again, you see that the visibility for the reference is not saved.
This is because the system variable VISRETAIN is set to 0. You need to change the variable to 1.
Changing system variable
If you are not familiar with changing system variable, type VISRETAIN at command line then press [enter]. Type 1 then press [enter].
About changing reference file layer visibility
If you never work with reference file visibility before, you can manipulate the visibility from master file. You don’t need to open the reference file to turn off/freeze layers.
From layer properties manager, you can see layer list from a reference file by selecting from filters. In the layer list, you can see the layer name has the file name as prefix.