You could use something for itch back there, but she can't lick it, so an ecollar or something would probably have to be used. Your vet can recommend a product if you want to do it.
Nah, you didn't hurt her by emptying them. I know people are nervous about doing this, but it is not easy to cause damage... As she gets older, they may (or may not) need to be emptied and it is ok for owner to do it; but as always, ask your vet if it is ok. You emptied them externally. She probably emptied them internally. Both acceptable. You can probably get more out internally. Some are opposed to putting their finger in there, esp. with small dogs. I use both methods.
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