A method of making an insulating glass (IG) window unit includes: having a coated article including a multi-layered low-E coating on a glass substrate; at least two flexible protective sheets adhered to a top surface of the low-E coating via at least an adhesive layer, and a protective coating over the low-E coating and/or over at least one of the flexible protective sheets in order to substantially fill one or more gaps formed between the low-E coating and the flexible protective sheet(s) and/or between the flexible protective sheets; and following cutting, edge seaming, and/or washing, removing at least part of the temporary protective coating by peeling the protective sheets off and removing at least part of the protective coating when peeling off the protective sheets.