I’ve noticed a library created in Halion 6 for Halion Sonic works only in version 3 and not version 2. Is there a particular reason for this, or am I doing something wrong? 
An answer would be A W E S O M E 
Halion as most Steinberg products is backward compatible. Halion 6 can open both factory and user presets created in earlier versions.
But this doesn’t work the other way around.
Can you load any of the new factory libraries of Halion 6 in Halion 5?
HSSE 3 was released to be able to use user created libraries, which wasn’t possible before.
So I guess the answer to your question is, user created libraries will only work in the latest version of Halion instruments.
T H A N K Y O U