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This is example project : https://pasteall.org/blend/7a092c98a4c1485a8aaed35b16219108

If You apply skin modifier to it, You will notice mesh gets distorted, creating hole in model. I struggle with this problem for very long and I usually solve it by applying mirror modifier first. But this is unconvenient. How do I prevent this from even happening ? Am I using skin modifier wrong ? Is it about modifier order ?

Generally I wish to keep workflow to create base shape with skin modifier, create armature using skin modifier, tweak model in subdivision modifier, add final details without subdivision modifier, finally add unsymetrical elements without mirror modifier

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    $\begingroup$ What do you mean with "this is inconvenient"? This is the normal behaviour of modifiers. The order matters. So different orders will create different results (with just a few exceptions). So if you apply the skin modifier first, of course you will get a different result, because by this you first apply your skin and then Blender uses the mirror modifier. Before applying Blender uses first the mirror and then the skin modifier. $\endgroup$
    – Chris
    Commented Mar 5, 2022 at 12:37
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    $\begingroup$ If this is normal I guess I am not worried :). I thought, that result of applying should be visually the same as before applying. Thank You for clearing this for me $\endgroup$ Commented Mar 5, 2022 at 12:49

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This is the normal behaviour of modifiers. The order matters. So different orders will create different results (with just a few exceptions). So if you apply the skin modifier first, of course you will get a different result, because by this you first apply your skin and then Blender uses the mirror modifier. Before applying Blender uses first the mirror and then the skin modifier.

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