This was happening because in `apply_eval_grease_pencil_data`
we gather all the potential original layers to clear. This was done
by taking the set of all original layers and then removing layers
from the set that map to an evaluated layer.
The remaining layers are unmapped and should be cleared.
The problem is that invisible layers are no longer part of evaluated
data so there wouldn't be a mapping that could be found.
To fix this, we don't initialize the set of `orig_layers_to_clear` to
all the layers, but instead to only the layers that are visible.
This will ensure that we don't clear keyframes of hidden layers.
Pull Request: https://projects.blender.org/blender/blender/pulls/135121
ddced37ea4