Problem statement

When you import a bones in an existing skeleton, the skinned bones origin are set to 0,0.
I'll provide picture, I hope they will help you understand better the problem.

So, here is my step about the bug :
1) Create at least one bones
2) Put it in a skin
3) Export it
4) Create a new project (You can stay in the same project though, it's just to make everything clear)
5) Import the previously exported project in the existing skeleton. You can check either "Replace" or "Ignore" in the option, it won't change anything.
6) The project is imported, but skinned bones position are reset to 0,0

Here is four ... it was an ears before but anyways, here are four ...thing.
The grey one is completly free of skin. The mesh is weighted to the bones.
The red one is completly skinned in "skin 1" (Yes I am a creative as you can see), and the mesh is weighted too. (They are all weighted actually)
The green one got two bones skinned at "skin 2", leaving 1 unskined. Weighted as well.
The blue one got one bones skinned at "skin 3", leaving 2 unskined. Weighted as well.
Expected Result

If you import it in a new skeleton / project, everything is fine. But, even if it's a fresh new empty project, if I import it in a existing skeleton, here is the result :
Expected Result
As you can see, the red bones are now all in 0,0 position. Two green (the skinned one) are also at >! 0,0 and the only bones that was skinned for the blue one is at 0,0 too.

I used three different skin but it did the same with only one skin too.

I didn't get any error so I can't give a spine.log...
I can shared the exported JSON though, even if I don't think it will help you that much :

{
"skeleton": {
"hash": "lC9AKtYPrrk",
"spine": "4.2.09-beta",
"x": 379.12,
"y": -819.96,
"width": 916.86,
"height": 468.29,
"images": "",
"audio": ""
},
"bones": [
{ "name": "root" },
{ "name": "bone", "parent": "root", "length": 248.36, "x": 500.74, "y": -449.08 },
{ "name": "bone2", "parent": "bone", "length": 196.74, "rotation": -0.72, "x": 248.36 },
{ "name": "bone3", "parent": "bone2", "length": 157.38, "rotation": 0.72, "x": 196.74 },
{
"name": "bone4",
"parent": "root",
"length": 248.36,
"x": 500.74,
"y": -753.99,
"skin": true,
"color": "ff0000ff"
},
{
"name": "bone5",
"parent": "bone4",
"length": 196.74,
"rotation": -0.72,
"x": 248.36,
"skin": true,
"color": "ff0000ff"
},
{
"name": "bone6",
"parent": "bone5",
"length": 157.38,
"rotation": 0.72,
"x": 196.74,
"skin": true,
"color": "ff0000ff"
},
{ "name": "bone7", "parent": "root", "length": 248.36, "x": 500.74, "y": -1105.63, "color": "06ff00ff" },
{
"name": "bone8",
"parent": "bone7",
"length": 196.74,
"rotation": -0.72,
"x": 248.36,
"skin": true,
"color": "06ff00ff"
},
{
"name": "bone9",
"parent": "bone8",
"length": 157.38,
"rotation": 0.72,
"x": 196.74,
"skin": true,
"color": "06ff00ff"
},
{ "name": "bone10", "parent": "root", "length": 248.36, "x": 500.74, "y": -1422.84, "color": "009fffff" },
{ "name": "bone11", "parent": "bone10", "length": 196.74, "rotation": -0.72, "x": 248.36, "color": "009fffff" },
{
"name": "bone12",
"parent": "bone11",
"length": 157.38,
"rotation": 0.72,
"x": 196.74,
"skin": true,
"color": "009fffff"
}
],
"slots": [
{ "name": "bone", "bone": "bone" },
{ "name": "bone2", "bone": "bone4", "color": "ff0000ff", "attachment": "bone" },
{ "name": "bone3", "bone": "bone7", "color": "1aff00ff", "attachment": "bone" },
{ "name": "bone4", "bone": "bone10", "color": "00a6ffff", "attachment": "bone" }
],
"skins": [
{
"name": "Skin 1",
"color": "ff0000ff",
"bones": [ "bone4", "bone5", "bone6" ]
},
{
"name": "Skin 2",
"color": "17ff00ff",
"bones": [ "bone8", "bone9" ]
},
{
"name": "Skin 3",
"color": "00b0ffff",
"bones": [ "bone12" ]
}
],
"animations": {
"First": {
"bones": {
"bone": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone2": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone3": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone4": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone5": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone6": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone7": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone8": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone9": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone10": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone11": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
},
"bone12": {
"rotate": [
{},
{ "time": 0.6667, "value": -15.98 },
{ "time": 2, "value": 17.68 },
{ "time": 2.6667 }
]
}
}
}
}
}