There isn't any difference... except that they're different lists. They're the same collection structure, same type in the collection, just different instances.
For example:
public PetSanctuary
{
public List<String> catNames;
public List<String> dogNames;
}
except with a user-defined type instead of String.
Edit:
Example hbm file
Code:
<class name="A">
<id/>
<bag name="list1">
<key column="aId"
<one-to-many class="B"/>
</bag>
<bag name="list2">
<key column="aId"
<one-to-many class="B"/>
</bag>
</class>
However: The above does not work because the database does not see the lists as separate, since all they have is a foreign key... so when you repopulate the lists, both lists will have all items from both lists in them. This is easily solved by a discriminator, except that the only way to populate a discriminator value (that I've seen) is to use subclassing, which is not a good thing in this case.