My sister went over to give Cyrus a cuddle today, and he snarled and bit her (more of a nip, not enough to draw blood or anything). This seems to happen a lot. At first I thought that he must be in pain (she mostly touches either his shoulders or flanks), but when my dad or I pet him there, he actually seems to
like it.
We have tried time-outs and a myriad of verbal reprimands, etc., but he just keeps on reacting to her affectionate gestures in a hostile manner. She is very enthusiastic about petting and cuddling him, but has never been ungentle with him. The only difference between the way she handles him and the way my dad and I handle him is that she cuddles him more, picks him up, kisses him, hugs him...etc...
Is the NILIF program something done throughout a dog's life? I became complacent and eventually stopped when he seemed to become more obedient (eg., faster to perform, and so on). My sister gave him a time-out alone in the bathroom for snarling at her before, and it seemed to work. Now, however, it's like he has become desensitized to her verbal reprimands and time out.
Any adive would be greatly appreciated!

Thanks in advance.