### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

}
		}
		if (s.attribute_buffer != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(s.attribute_buffer);
			s.attribute_buffer = 0;
		}
		if (s.skin_buffer != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(s.skin_buffer);
			s.skin_buffer = 0;
		}
		if (s.index_buffer != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(s.index_buffer);
			s.index_buffer = 0;
		}
		if (s.versions) {
			memfree(s.versions); 
		}
		if (s.lod_count) {
			for (uint32_t j = 0; j < s.lod_count; j++) {
				if (s.lods[j].index_buffer != 0) {
					GLES3::Utilities::get_singleton()->buffer_free_data(s.lods[j].index_buffer);
					s.lods[j].index_buffer = 0;
				}
			}
			memdelete_arr(s.lods);
		}
		if (mesh->blend_shape_count) {
			for (uint32_t j = 0; j < mesh->blend_shape_count; j++) {
				if (s.blend_shapes[j].vertex_buffer != 0) {
					GLES3::Utilities::get_singleton()->buffer_free_data(s.blend_shapes[j].vertex_buffer);