Zippy Wonderdust

I think I found the "problem".  I did some testing in a randomly generated creative-mode world that has all the same mods as I usually play with. I spawned in a few Bowtorns and some moose and did some target practice with a longbow. I then came at it systematically from different distances and angles.
I find that when harvesting a dead mob I now have to get super close for it to work.  It is no longer enough to rely on your crosshair turning red; it can be red and you can still be too far away.  I have to get as close as possible to the geometric center of the creature (close enough so that I'm actually pushing it across the ground) to get a reliable result. This means aiming for the midsection of a Bowtorn, even though I might get a red reticle over the head or lower body.  Same goes for the moose; only the belly, approached from the side with the legs, gives reliable results.
I didn't test any other mobs, but I suspect all of the larger ones may need this approach.

...and more testing was done.
Scratch my earlier musings as absolutely wrong.  I made a world with 90% ocean cover and used the various letters and maps to locate the resonance archive and two other locations (trying to avoid spoilers).  Each location spawned on an island that had very obviously been generated just for them; each island was roughly circular and was approximately 1000 blocks in radius.
On the bright side, they *did* all spawn correctly in what I would consider some pretty non-optimal circumstances, which makes me wonder what went wrong for @Joseph Goulakos...

Using this Reddit post as a reference, you could (at least temporarily) reduce your save file size by using the following commands to 1) remove all chunks from the database that players have explored but not significantly altered, then 2) drop the pruned data from your save file and compact it.
(Back up you data first! If this borks your world and you don't have a backup to restore from, it's *not* *my* *fault*.)
/db prune 16 drop confirm /db vacuum