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I have window elevations where I hide the casing (trim) around the window with the linkwork tool using <invinsible> lines. and it seems as though next next I have to open the project the lines that I hide with the linework tool have reverted back.
Have you checked if this is specific to the project you are working on or the family (e.g. test in a new project with one of the included window families)?
I tested this in Revit 2014/2015 (new architectural project, with a Fixed 36" x 48" window) and I did not see a change in the lines modified by the Linework tool (after closing and reopening the project).