ISOLATEOBJECTS or HIDEOBJECTS command changes remain applied after saving and reopening the drawing? Or elements not respecting Layer controls between drawing sessions?
Check the OBJECTISOLATIONMODE variable as this variable controls whether hidden objects remain hidden between drawing sessions.
If you require Isolated/hidden objects are temporary for current drawing session – Set to 0 (Default)
Isolated/hidden objects persist between drawing sessions - Set to 1 (Dangerous)