Jelly like, clear stool is usually a sign of muciod enteritis. Its easily treated with biosol, or neomyacin if its caught right away. You mix both medications 1 teaspoon per gallon of water, and add it right to the rabbits water. Surringe feed it every half hour till the illness clears up if you have to. You can also pick up dri tail at just about any pet shop or meijers, and give it to her every half hour till it clears up. Also give her some clean straw to eat. it will help clear up the diarrhea. I would not wait around to treat her either. cause this stuff will kill the rabbit within a matter of hours. Get her on medication ASAP.
Since you are raising rabbits, I suggest you get a current copy of the guidebook to raising better rabbits and cavies. It has a great medical section, and will help you out a lot with a sick rabbit. Its something that no rabbit breeder should go without. You can get it for free by joining the ARBA. Or you can purchase it off their website.
www.arba.net
You need to keep your rabbits on the pellets. Going without for one day is fine. 2 days is not so good. Letting them go like that will take the condition off the rabbit. And yes there is a good chance it will get sick.
As far as the information that was provided to you from the HRS (Rabbit.org), do not trust anything that is from that website. It is often incorrect and biased. They are a rabbit rights organization. Especially the part about feeding them, as a lot of rabbits can get very sick from being fed that. They do not need a timothy based pellet. In fact, many rabbits, including pet ones cannot handle eating timothy pellets. I am not sure how big this rabbit is, but I know I feed my five pound standard chins, Florida whites, and Thriantas all 1 cup of pellets per day. What was recommended is not correct. feeding very little pellets like that will do more harm to the rabbit then good. You need to feed it a good quality pellet, that is high in fiber, and what it will clean up in one day. Also make sure the feed is low in protein. When you buy feed, make sure you buy enough so that you don't run out.
What type of hay are you feeding? If its alfalfa, then might be your problem. Feeding too much alfalfa will cause enteritis problems. Alfalfa is a great hay to feed as long as its done properly. It should be fed once a day, or once every other day in small amounts (a handful). Sometimes it is best to substitute timothy hay for the alfalfa as it is better for them.
And as far as losing the litter goes, it happens. All rabbits will lose litters now and then. So there is no reason for people to yell at, or lecture you over it. Rabbits are a prey species. You can breed the doe again after its lost the litter. I bring my litters inside at night, and take them out to the does in the morning. Even then, I still lose babies. Sometimes you can do what you can, and you will still lose them. Heck Ive lost two litters, and had three live ones this year. The first was due to an inexperienced Mom. The other was from a proven doe that I bred and raised myself. She decided to lay on them in the nest box after she gave birth. Both were rebred right away. The young doe had a successful litter of seven this morning, and the other is due in a couple of weeks.
Also bringing the next box to the doe during the day will not cause her to abandon them. You'll find she'll be very 'angry' when she sees her babies brought to her, and will jump right in and feed them.