Carox,
I always recommend for the people to tap on their negative emotions on what seems to be an "animal issue". If our relationship with our pets is not at all like we hoped it would be - we do experience a wide range of negative emotions. Be it sadness, frustration, anger, guilt etc - I see them as normal emotional responses to a challenge our pets present for us. Sometimes our expectations are just not realistic and place an unfair load on our animals. So, for you and your mum: tap on your emotions first. You could use the Choices Method to tap in more patience for example, or a greater ability to accept the cats just the way they are.
I would not make any attempts to stroke the bigger cat at all. Like you explained, she shows you a very, very strong fear based reaction every time to force petting on her. Despite your best intentions, you inadvertently, yet powerfully reinforce her view of humans as scary and untrustworthy (since you do ambush her in order to pet her). It is actually classical conditioning going the wrong direction. Petting does become something of a nightmare for her and each episode strengthens her negative view of humans. I know it is hard, but let her come to you. Give her all the time and space she needs, assist her by tapping surrogately on her emotions. If and when she comes and asks for some stroking: do so in TINY increments. You want to end it before she feels overwhelmed again. One or two brief strokes, perhaps with just one finger and let her be.
Allow both of them to discover the joy of close contact with humans, to enjoy the trust and the physical sensations. But also allow them to be who they are. Not all cats love petting and stroking. My cat always wants to be close by, but she is doesn't care for petting, stroking or sitting in my lap. She is not afraid, she just doesn't like it. It was a bit of a challenge for me to let go of what I wanted from her and allowed her to be my "untouchable cat"
I would also use the Choices Method for the cats, adding "calm and confident no matter what" as the positive choice. Or just standard EFT:
even though I feel this horrible panic when my humans sneak up on me and grab me to stroke me, I am a great cat.
even though I can't think straight and use all my strength to escape and even bite them, I am really a very good cat.
I might tap on the bigger cat's weight and eating issues as well.
Once you start tapping, more thoughts will come to you. You can build your statements around the behavior you observe and you can follow your inner voice. Chances are you will need to tap daily for a while, sometimes it can take weeks to really see a change. And sometimes change happens very quickly. Just be careful about "trying harder". This is not about putting pressure on you or your cats, it is about a change in their perception about the world they live in. Try not to hold on to fixed ideas about how cats should be, be open to whatever they choose to be. We are not that much different: if somebody tries to change us into something we are not, we don't appreciate those efforts.
I don't see any reason why you would need to decide between flower remedies and EFT. You can use both. The only disadvantage would be that you would not know for sure what actually worked.
Good Luck!
Gitta