I have only limited experience with looped (no .kf files) animated weapons (particles, mesh translations/rotations), body parts (wings/neck; mesh translations/rotations and morph), hair (particles, mesh translations/rotations) as well as with animated activators (I prefer to use scriptable activators, not static actors). There are some problems (I cannot exclude Max exporter issues) but in general that works fine.
What's that? I know only theses Phijama's shields: NiAlphaController, NiUVController NiGeomMorpherController phijama (Phoenix shield, Obsidion shield and shield from Dragon Blade mod). There are no "blocking animation" in these mods.
But here is the devastating part:
From my preliminary tests I can confirm that "merge_kf.exe" is messing up all fighting animations, spell animations, and one-frame animations like "InventoryWeaponOneHand". I have to perform more tests.
However, I have no problems with merging walk/run/jump(swim not yet tested).
I have not yet performed extensive testing of that but in the past I was able to merge correctly walking/running forward animations with idels.
I will post results of my investigation as soon as I get something solid.