Very interesting. We're hitting some odd edge cases here, which I think can easily be avoided. I don't believe this is necessarily related to the art pipeline update, but if it is - it's something which probably shouldn't have ever worked

That last asset, the swinging pendulum you made the video of, IS playing the full animation. It is merely offset. Using arbitrary values to explain what I'm seeing:
Say it rotates between +15 degrees and -15 degrees around the X axis. The viewer shows frame 0 as rotated to +15 degrees and frame 99 as -15. In Heroblade, it is appears that frame 0 is 0 degrees and frame 99 is -30. So the full thing, but offset.
When you create animated assets, you should create the bone that they are attached to manually. This will be automatically created by the export, but you have no control over the orientation. Try creating the bone and skinning the pendulum to it while the pendulum is vertical. Then create the exact same animation and see if it displays properly in the engine.