The "Show Hidden" action automatically removes the marks on the files so that I cannot toggle between "Hide Marked" and "Show Hidden".
Each time I use "Show Hidden", I have to redo the individual file Mark +"Hide Marked".
Is there a way to persist the Mark on the files?

I have never used the Mark feature by myself.

According to the short explanation available for those context menu items it looks like this feature is just for adding files to a list of files to ignore for folder comparison and hide them. With using Show Hidden all ignored files are displayed again and the marks are removed from all files, i.e. the list of files to ignore is cleared and the user must recreate it.

From a user's point of view it would make sense to keep the "mark" list and just make the ignored (hidden) files visible again with keeping the "marks". I suggest to contact IDM support by email regarding this feature for clarification and suggestion of an improved management of marked files in a near future version of UC.