This sounds like it could be a coordinate system or Y-axis handling change introduced in the 4.3 runtime or the newer Godot version. A few things to check and try:
Check your skeleton's Y-down setting
In spine-cpp (which powers spine-godot), the Y-axis orientation is controlled globally:
Bone::setYDown(true); // Affects all skeletons
If this setting changed between versions, it could cause bones/slots to appear flipped on the Y axis. It's worth checking whether the spine-godot 4.3 runtime initializes this differently than 4.2 did.
Try flipping the skeleton scale instead of individual slots
Rather than fighting individual SpineSlotNode scales, you could try compensating at the SpineSprite level by adjusting its scale in Godot's scene tree (e.g. setting the SpineSprite node's scale.y to -1). This is a workaround at the node level rather than touching the Spine runtime directly.
Check get_global_bone_transform / set_global_bone_transform
If you are using bone transform helpers, note that the SpineSprite documentation mentions:
A retrieved or set transform will not encode skew.
And transforms should be set before world transforms update, via the before_world_transforms_change signal. A version change could affect how these transforms interact with the canvas coordinate space.
Verify your export settings
Make sure your Spine 4.3 export is clean — re-export both the skeleton data and the texture atlas fresh, since sometimes stale data from a previous version can cause unexpected flipping behavior.
What's likely happening
The Y-axis flip on sub-slots is most likely a coordinate system mismatch introduced by either the Godot 4.7 canvas space changes or a change in how spine-godot 4.3 maps Spine's Y-up coordinate system to Godot's Y-down coordinate system. This is a known pain point when upgrading across both Spine and Godot major/minor versions simultaneously.
Could you share a minimal reproducible scene if the above doesn't help? That would make it much easier to pinpoint whether the issue is in the runtime itself or in how your specific skeleton data is being interpreted.
