ok, how about this: go ahead and create a style sheet for those apostrophied lines, even if that style sheet doesn't do anything to change the text formatting. you're just going to use the style sheet as a label. apply it to the lines in question.
then, in quark's find/change dialog, uncheck the "ignore attributes" box. this will expand the window to show more search options.
in the "find what" column, enter your text (in this case, the apostrophe) and select the style sheet you created. then, in the "change to" column, enter the prime mark.
this will tell quark to search only those passages that are styled appropriately, leaving the rest of your document unchanged. (remember, Quark's S&R is sometimes persnickety; place the cursor at the beginning of the document's firstmost text box to make sure the search starts from the beginning.) when you're all done, you can delete your dummy style sheet if you're not going to use it for actual text formatting.
granted, it's a bit of a process, and if you're going to go through every instance and apply a style sheet you might as well just change the punctation while you're there... but this way you know you won't miss any.
hope it helps!