Created attachment 118936 [details]
Test .kra file

SUMMARY
When you merge layers from the example file in the order provided in the "steps" section, the merged layer will be appear at the top of the layer stack instead of being one layer below. Thus the projection is different before and after merge.


STEPS TO REPRODUCE
1. Open the provided file.
2. Select layers: Layer 5, Layer 3, Layer 2, Layer 4. (For example: select layer 5; hold Shift; select layer 4.) The active layer must be layer 4.
3. Use shortcut (default: ctrl+E), Layer -> Merge with layer below, or right-click on the layer 4 (important!) and select "Merge with layer below".

OBSERVED RESULT
The result layer appears on top of the layer stack instead of the correct position.

EXPECTED RESULT
The result layer should be one layer below the top of the layer stack.

NOTES: 
- If layer 5 is selected or you right-click on layer 5, the result layer will be in a correct position.
- If you undo, the selected layer will be only Layer 5 and Layer 3.

The test file is a modified version of a file from bug 405366.


Krita

 Version: 4.2.0-pre-alpha (git fbba406)
 Languages: pl
 Hidpi: false

Qt

  Version (compiled): 5.11.3
  Version (loaded): 5.11.3

OS Information

  Build ABI: x86_64-little_endian-lp64
  Build CPU: x86_64
  CPU: x86_64
  Kernel Type: linux
  Kernel Version: 4.15.0-45-generic
  Pretty Productname: Linux Mint 19.1
  Product Type: linuxmint
  Product Version: 19.1


Hardware Information

  GPU Acceleration: auto
  Memory: 7771 Mb
  Number of Cores: 4
  Swap Location: /tmp

ADDITIONAL INFORMATION
Git hash: fbba406b15d7f6b066fd40