I have had my cats almost since birth, and they are now approximately ten years old. They are very friendly with me and let me touch them anywhere, especially if it involves belly rubs.
After diagnosing one of my cats as having allergies, I now have to give her medication every day. It is liquid, but I put it in a size 4 gelcap (very small) and use a pill popper to get it in the back of her mouth. I then hold her mouth closed until she swallows, so she does not spit it back out. This is obviously an uncomfortable act for her, no matter how necessary it is.
This causes a problem. While she allows me to pet her and give her belly rubs, she freaks out any time I pick her up. If she is sitting on the floor and I walk over to her, she hides from me. If she is laying on the couch or a bed, she does not seem to mind me approaching. Clearly, the daily medication ritual has her unnerved. She is still friendly to me, however, she tries to avoid contact if she thinks it is medicine time.
I did read a few other questions about similar issues, but they are all centered around a new cat. I have had her for almost a decade, and this behavior is new. I would like for her to trust me again. This is not so much about gaining the trust and affection of a cat, but regaining her trust - she is still affectionate to me and will even jump into my lap. I just have a difficult time picking her up or approaching her at times.
Her allergies require daily medication for the rest of her life. Her allergy is not one that I can eliminate via environmental changes. After consulting with the veterinary allergist, the only available medication for cats is liquid Atopica (which I put into a gel cap for easier administration). Unfortunately, this is not an issue I can address via the root cause (daily pills) and I must address the behavioral aspect.