Hi! My rabbit had this same issue a few weeks ago, he was constantly taking off his cone! He did not like it at all, he would not move or jump around like before but once that cone was off, he was as happy as can be! I’m sure she’ll be fine once this is over! To build trust again, try just taking off the cone once a day for a little while and watch her. Mine would not leave the stitches alone, so I had to closely supervise. You can also try giving her treats after you give her medicine so she associates it with something good!
Good luck and happy healing!