How to make my conure not so cautious with me

I have a green cheeked conure that I have had for about 2 months, and she is amazing. Everything is right with her, she's friendly, cuddly, doesn't bite but qirky as well. She really loves my company, and has bonded with me more than everyone else, she usually loves cuddling with me and jumps on my fingers as soon as I come to see her, she loves scratches and is really happy, but I notice that whenever I do something she doesn't like, like take her off my wire shelf or put her in a carrier, as soon as I take her out, for the next day or two it's like I just got her. She runs away from me, won't go on my fingers, doesn't want to come out with the rest of the family and sits on top of her cage. She usually goes back to her rambunctious self the next day or two, but it's really sad when I feel like I've completely ruined her trust in me. I know that birds do hold grudges, but is there a way to make Bobbie less scared after I do something she doesn't want.

As long as your are not forcing unwanted contact or legit scaring here, you are fine...Are you toweling her to get her off the shelf, or grabbing her? Because that does harm trust/scare a bird. If she is stepping up and then you put her in and she's annoyed, that's fine (probably, as long as she isn't genuinely scared of the carrier, and if she is, that is something you train for gradually via positive associations and slow exposure). Another thing, try not to follow predictable patterns when picking her up (sometimes pick her up and don't put her back in the cage/carrier after she has been out for awhile).

If she is going up there and you are having to pry her down/ struggle/use force, then you need to cover that shelf or make it less appealing so that this doesn't happen whenever she is out. A slight prying of the toes w/out biting is okay, but grabbing, toweling/forcing should be avoided.

Do you let her go in and out of her cage without locking her up the second she's back in? Lots of people mistakenly shut the door on their bird the second the bird goes in voluntarily (like, "YES, GOT HER!") but that is harmful because it teaches the bird that anytime he/she enters her cage, she will be locked up, which leads to avoiding it unless they are placed in there against their will (which is something to avoid).

When you say carrier, do you mean a carrier or cage? If you mean carrier, why are you putting her in a carrier all the time (just curious). That can be scary for some birds if they associate it with the vet, leaving etc..or if it's a new and unfamiliar carrier in comparison to her cage.

Just like a kid, they will get mad about stuff they don't want to do, but the key is differentiating legitimate fear/upset from pouting because they didn't get their way.

Also-- It sounds like your bird is young, but make sure that you don't allow access to shadowy spaces in or out of the cage (huts, boxes, low shelves, under furniture, in bedding etc etc).. These will become hormonal triggers at sexual maturity (and subsequent behavior triggers), and you don't want her to get used to things that won't be acceptable within a few months. It can also be particularly hard to remove a bird from a nest-like space when they are hormonal, and that is not a fun struggle to have (and it stresses out the bird, so just telling you as a heads- up in terms of what you should be thinking about for the near future.
When you say cuddles, make sure you are only petting on the head and neck. The rest is reserved for a mate in the wild and you don't want to be perceived that way.
Prolonged petting in places other than the head/neck and access to snuggle huts, shadowy spaces etc, can also lead to health consequences in females, such as egg-laying (and potential egg-binding).

You've had Bobbie for two months, do you know her age? Seems you have not ultimately lost her trust, more like a cyclic tantrum. Some of that may be associated with relative newness to you.

Bobbie was around 6 weeks old when we got her, and we've had her for two months after.

You definitely have to do everything positive and use positive reinforcement. So like for the travel cage have your bird go in and come right back out with lots of praise and treats. Repeat a few times throughout the day. Just make it part of your daily activity, lots of praise! I use safflower seeds as my go to treat! GCC love them and they are small and easy to give just one.

When she goes somewhere she shouldn’t, just ask her to step up give her a test move Gerri a different spot and give her a treat again and tell her how good she is.

Also set her up for success, set up a few areas fir her to hang out that are more desirable to gen the bad places. I use ceiling hooks and fishing line, then attach a rope bungee or rope hoop st eye level. Or they sell metal stands that you can attaché perches to that you can move around. Having places that they can use as their own “ furniture “ makes everybody happy.

GCC will learn to use their beak to scold you, especially ias they get older... and get can loose trust when they think they have been wronged . The best ay to prevent hurt feelings is explain things to them, pay attention to their body language and respect they are their own person and they are smart. Don’t grab them up and move them be so you can ( especially babies) because they will resent that. So ask for them to step up and praise, ask them to go into pet carrier and praise.

Parrot = Three year old non verbal human with ADHD dressed in feathers. Understands 100 or so different words/phrases. Depending on species of course. Only way to communicate is biting, shrieking or facial expressions. Again depends on species but is about right for a GCC.

If you alter your view to "How would a human toddler react if I did ..." some of the behaviour will make more sense. Bright up beat talking when praising. Favourite treat when they do something you want them to. Short time outs when they do something you don't want them to. These work with parrots as well as with 2 or 3 year old humans.