Merge Visible Didn't Merge All Visible

I just had something happen that I had never had happen before.

As I have done many many ties before, when a stack of layers gets so large that it takes forever to save the image, and I have used merge-visible+ALT several times throughout the stack, I make one layer on top that is all layers below merged into one; I save this stack as   picture_B29_Stage_1;   I then select all the other layers and delete them; I then save this remaining top layer as    picture_B29_Stage_2   and continue my project from that point.

I may have as many as five stages by the time the project is complete; working in stages really speeds things up.

Well, just a bit ago, I made my top-of-stack layer, then selected and deleted all the other layers.........>>>!!!!.......WHOA THERE; I am seeing transparent background in three spots.

I clicked "undo" and un-deleted the layers.

One-by-one, I turned off visibility of each layer, until I found the one that had been plugging the hole; it was second up from the bottom background.

I don't see how this could have happened, as I had merge-visible+ALT several times above that layer.

I did another merge-visible+ALT on top of everything and this time there were no holes.

Funny things happen when you are messing with computers; I am just glad the holes were large enough that I easily spotted them; had the holes been smaller or better camouflaged I may not have caught the problem.

I may never know why or how this happened; I just thought I would share my experience in case it may be of benefit to someone else down the road.

Thanks for reading.