I have never owned Patagonia waders, but my experiences with other Patagonia products I own is similar to yours. The waterproofing on my old SST rain jacket, for example, wore out after over 10 years of use and when I inquired about gettting it repaired they sent me a new one at no charge.
I have several pair of Simms waders, and other Simms products, and have been buying Simms waders for (what?) 20 or more years. So, it should be obvious that I like their products. However, invariably when I return anything to Simms for repair, even after 2-3 years of moderate use, I always end up being charged for the repairs.
After Simms charged me about $75 for repairing numerous pin hole leaks in my 2 year old waders about 3 years they developed more leaks soon afterward. (Personally, I think it was the material, not the usage that caused the leaks, but that's another story.) So, I got a tube of Aquaseal and used the entire tube on about 50 areas that looked like places that might be leaking. The waders have been bone dry ever since ---at least that should be a testimony for the effectiveness of Aquaseal!