A method of making an insulating glass window unit, the method comprising: forming a multi-layered low-E coating on a glass substrate, wherein the low-E coating comprises at least one infrared reflecting layer comprising silver sandwiched between at least first and second dielectric layers; adhering at least two flexible protective sheets in non-liquid form to a top surface of the low-E coating via at least an adhesive layer to form a protected coated article; applying at least one protective coating in liquid form directly on the low-E coating and/or over at least one of the flexible protective sheets in order to reduce one or more gaps formed between the low-E coating and the flexible protective sheet(s) and/or between the flexible protective sheets; following applying and curing of the protective coating, shipping the protected coated article to a fabricator of IG window units; the fabricator cutting the protected coated article into an appropriate shape and size with the protective sheets thereon, edge seaming the protected coated article with the protective sheets thereon, and/or washing the protected coated article with the protective sheets thereon, so that following the cutting, edge seaming, and/or washing the protective sheets and protective coating remain at least partially adhered to the top surface of the low-E coating; following said cutting, edge seaming, and/or washing, peeling the protective sheets off of the top surface of the low-E coating to form an unprotected coated article, and also removing at least part of the protective coating when peeling off the protective sheets; after peeling the protective sheets off of the top surface of the low-E coating, thermally tempering the coated article including the glass substrate and low-E coating; and after said tempering, coupling the tempered coated article including the glass substrate and low-E coating to another glass substrate to form an IG window unit. forming a multi-layered low-E coating on a glass substrate, wherein the low-E coating comprises at least one infrared reflecting layer comprising silver sandwiched between at least first and second dielectric layers; adhering at least two flexible protective sheets in non-liquid form to a top surface of the low-E coating via at least an adhesive layer to form a protected coated article; applying at least one protective coating in liquid form directly on the low-E coating and/or over at least one of the flexible protective sheets in order to reduce one or more gaps formed between the low-E coating and the flexible protective sheet(s) and/or between the flexible protective sheets; following applying and curing of the protective coating, shipping the protected coated article to a fabricator of IG window units; the fabricator cutting the protected coated article into an appropriate shape and size with the protective sheets thereon, edge seaming the protected coated article with the protective sheets thereon, and/or washing the protected coated article with the protective sheets thereon, so that following the cutting, edge seaming, and/or washing the protective sheets and protective coating remain at least partially adhered to the top surface of the low-E coating; following said cutting, edge seaming, and/or washing, peeling the protective sheets off of the top surface of the low-E coating to form an unprotected coated article, and also removing at least part of the protective coating when peeling off the protective sheets; after peeling the protective sheets off of the top surface of the low-E coating, thermally tempering the coated article including the glass substrate and low-E coating; and after said tempering, coupling the tempered coated article including the glass substrate and low-E coating to another glass substrate to form an IG window unit.