I've been having similar loss of appetite and weight loss problems with Chloe ever since she got her URI about a month ago. I too ran a fecal sample and it was negative also.
I got her mouth checked out several times, and the vet felt that there was no indication of anything oral and that gassing her to get a closer look wasn't neccessary. I have heard people say sometimes oral tumours/problems cannot be detected unless the hedgehog in under sedation, so if you do decided to sedate her anyways for the xray/bloodwork, make sure the vet looks at her mouth very closely too.
I also tried cutting kibble up (I used a pill cutter - you can buy these at any drug store, and it worked very well) but like LG said I think Chloe was offended by the smaller pieces because she actually ate less! In fact, Chloe picks out the largest kibbles (natural balance green pea & duck and Innova kitten) first before eating the smaller ones, but she's just weird like that
My vet concluded that she was just being fussy and told me to put her on high fat, tastier kitten foods to see if that picked up her appetite. It took about a week for her to accept new foods but now she is eating much better.
Maybe you just need to try playing around with some higher fat foods for her until she finds something she really likes? Innova Kitten (these kibbbles are huge) is a big hit with Chloe, as is Now! and Go! foods and Before Grain Chicken formula (these are all around 20% fat content).
What I've also started doing is giving more bugs and higher fat bugs. I give 4-6 mealworms, 3-4 waxworms (very high fat content) and 1-2 cut up superworms per night. As well, I alternate offering meats, frutis and veggies (a teaspoon or less). I've tried wet cat food, wellness healthy indulgences, sweet potatoe baby food, fruit baby food and some fresh fruits and veggies so far. It takes a long time for Chloe to accept a new food, but I figure at least if the other foods are there, she has an option between that and the kibble. Maybe you could try the same with Emmy if the vet concludes there's no underlying problems?
I hope Emmy gets better and you figure out what's going on! I'd be very interested to hear what your vet comes up with.