Issue with saved photos

You need to view at 100%.

Whenever something seems to change when merging layers, it's because you are not viewing at 100%. The merged result is correct. The preview can be misleading and incorrect.

100% has nothing to do with size. It means one image pixel is represented by exactly one physical screen pixel.

Apparently you have a binary image where pixels are either black or white. Tonal adjustments have no effect on fully black or fully white pixels.

For performance reasons, all blending and adjustment previews are calculated on the on-screen version of the image. When you are zoomed out, that means a resampled and softened version of the image. Pixel levels are averaged out. You get a lot of intermediate values that aren't there in the full original data.

When you merge, commit an adjustment etc, the numbers are re-calculated on the full original data, pixel for pixel.

Viewing at 100% avoids all this and renders the whole issue moot. You see every pixel before and after, and so nothing changes.

We need more information. Can you describe the process of saving files, step by step? Have you tried flattening the image before saving if the layers are not important to you?