I don't have kids nor have I had to take or give medication myself, so take this with a grain of salt.
The first question I'd try to figure out is why she isn't taking them. Maybe it's a texture thing (my parents tried to give me omega 3 capsules, they were just generally unpleasant to take, blegh), or perhaps she doesn't understand what they do or why they are important (autistic people like to have concrete reasons for things rather than "because I said so" or "it'll make you feel better").