When I autoblend layers of images (focus stacked) and then disable the resulting masks the images are missing pieces like the mask doing permanent damage to the image it is masking - driving me balmy as my workflow is to create a blended image then go back to reinstate some areas with masks disabled - only to find that the disabled mask is not leaving image in tact as you would expect.
I reported something along these lines to Adobe many years ago - nothing happened with it. I found with the autoblend, PS bout just adjust the color of the masked area of a layer to blend in with the other layers and not apply the correction to the entire layer, so going back to edit a layer mask was impossible, due to the color shift.
Same experience. To be honest, Photoshop isn't very good with focus stacking. If you do a lot of it you might consider Helicon Focus or Zerene Stacker.
Yeah I had a look at Helicon but it doesnt seem to allow access to original layers - the whole idea is that I need to often reselect some areas like water for example that are better in a layer than the one chosen, not due to focus but perhaps just he way it flows.
If you have some layer, as you mentioned like the water, you could auto align the layers, duplicate the water one, then use auto blend on all except that one. Then manually blend in the water layer. I've had to do that often.
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