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I have tried EVERY combination of layers, masks, and available options that I can think of and I absolutely cannot get Auto-Blend to work properly on even the simplest example (a boat in the water). It always makes the boat (and anything else I've tried) mostly transparent. I've watched a half-dozen tutorials, I have Stack Images selected, have tried both Seamless Tones and Content Aware for Transparent Areas on and off, I've tried the boat with a layer mask, with the mask contracted and expanded, cropped with no mask, and I always get a result like the one attached. Does anyone have any suggestions to what I might be doing wrong? Thanks in advance.
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Stack mode is for focus stacking. Don't use that. Use Panorama mode for clean edges.
I use Auto-Blend on a daily basis and it works brilliantly. But you need to have a realistic starting point! The waves, with their high contrast and random patterns, will probably give some strange results, simply because you may be trying to blend extremely different values.
In this case you should probably remove the area covered by the boat from the underlying layer. Still no guarantee, it depends on how well the values match to begin with.