You can go through this article and get some clues : http://www.disabledrabbits.com/sore-hocks.html and this one too (as it has names of some bunny safe ointment list ) : http://www.disabledrabbits.com/urine-scald.html
Calendula cream, Neosporin (minus the pain relieving stuff ; the basic one), Silvadine and A&D Original Ointment are some of the ointments safe on bunny skin.
Since Cookies’ wounds do not sound too severe as of yet, you can apply the medicines twice/once a day. My bun Moshu had something similar. I wrapped her in a bunny burrito, kept her on my lap on my lap, got her in bunny trance and applied Neosporin on the affected area. I kept her that way for about 4-5 minutes. I know its very stressful for them..but the moment you will let them off, they will lick the medicine off.
Apart from ointments, this article suggests you can use bubble wrap in her cage. You can try this..though if it were my bunny, she would have torn that too.
Lets wait for the more experienced bunny parents here to give their responses.