The obly potential reason I can see for this is when a main (non parented, or “leaf”) bone is removed.
Removing something like a clavicle, would indeed damage the rest of the arm chain.
It is a mostly useless bone that an LOD less than 0 can surely do without, but its also the main bone that starts off the arm chain.
On the other hand - deleting a hand bone (just for pun sake) - would keep the whole arm working up until the hand.
Now, some of the new skeletal stuff is indeed bad - to where you can have something that should be a leaf/additional bone but ebded up being included into the chain.
As an example imagine a bicep.
Say you want it to pop out when you curl…
To do this, if you aplit the single bone humans have into 2, and set it up correctly, you can easily get the bulge to accentuate any time the rig curls (by popping out the juncion of the 2 bones).
Thats the $0.001 c way to do it, as it takes maybe 3 to 4 minutes to rig and weight paint - but obviously it also breaks everything apart as soon as you do something simple like enabling ragdoll…
And well, Epic is a big fan of the .0000001 c solution, so i can totally see situations where stuff like this is common.
The way to fix it is retargeting. You can peobably just map both bones to the same bone - and get rid of the bone.
Thats the same as just eating a bone and assigning its weight paint to another bone.
Assuming you retarget your animations or run them with the skeleton setup for real time retargeting, then it should not cause issues (aside from all the painstaking work to make it happen?)…
Aside from that, keep up the good work - and dont be afraid to take the whole thing out the engine into blender to analize things (or script bettter Python stuff!)