that's exactly what was happening to me, I noticed that some enemies had been disappearing from my game levels and I didn't know why.
I didn't know about the soul memory, but I'm guessing I'm still kinda fucked up on that side since I got a load of souls from helping a ton in the Forest of the Fallen Giants and Lost Bastile. (the first levels I've played, too)
In any case, a good source of titanite shards? I can't believe I need 2-3 hits to kill a mob from FotFG with a character in lv 91
They de-spawn after you kill them 10 times.
For titanite shards, They can be found pretty commonly from Harvest Valley. Which, might be the area you are in now most likely.
Here is some more info: http://darksouls2.wiki.fextralife.com/Titanite+Shard