Changeling is a characteristic-defining ability. It functions in all zones, not only while a card that has it is on the battlefield.

You put just one +1/+1 counter on Littjara Kinseekers and scry 1, no matter how many extra trios of creatures that share a creature type you control.

Three creatures share a creature type if there’s at least one creature type all three have, no matter what other creature types they have. For example, Littjara Kinseekers (which has all creature types), an Elf Warrior, and an Elf Wizard share a creature type because they’re all Elves.

If an effect causes a creature with changeling to lose all abilities, it will remain all creature types, even though it will no longer have changeling. This is because changeling applies before the effect that removes it.

The subtype Shapeshifter that appears on the type line is mostly there to reinforce the flavor. A creature card with changeling is just as much an Elf, a Dwarf, a Sliver, a Goat, a Coward, and a Zombie as it is a Shapeshifter.

If you don’t control three or more creatures that share a creature type immediately after Littjara Kinseekers enters the battlefield, its ability doesn’t trigger. If you don’t control three or more as the ability resolves, you won’t put a +1/+1 counter on Littjara Kinseekers or scry 1. The three shared-type creatures you control when the ability resolves don’t have to be the same three you controlled when the ability triggered.

If an effect causes a creature with changeling to become a new creature type, it will be only that new creature type. It will still have changeling; the effect making it all creature types will simply be overwritten.