Did you get any errors in the console when any of this was happening? If you try clicking on the Refresh Chunks button, does that rebuild the volume as you expect it to look?
I'm not sure what would cause you to have several frames in the hierarchy and only 1 frame in the animation, but you can delete the extra frames from the hierarchy. If those frames have information that you need, then I may be able to rebuild the animation for you if you send me your project.
I'm not going to lie, the editing tools need a bit of a re-work. Most of them are fine, but the brush tools have always been problematic. That's a big chunk of work and unfortunately I don't have time for that right now as I'm getting a game ready to exhibit this summer. (Note: that doesn't mean I have abandoned or am not supporting PicaVoxel, it's just that I can't spend the several weeks that an editing tool rebuild needs right now)
If you're finding that building animations using PicaVoxel is problematic, what I would suggest is considering using an external editor to build your frames (with MagicaVoxel or VoxelShop, exporting as .vox) and then importing them with PicaVoxel. There's a step-by-step in the manual for building animations by importing single frames from .vox files. You can then just use the PicaVoxel editing tools for small changes.
It's a bit of extra work, but it does mean that you are not relying on the Unity scene serialization to store your voxel models - you will always have them as an external file if things go wrong - much like building 3D models externally.