oh gosh! i'm so sorry to hear about this

i don't know if you're doing this, but instead of sterilizing the substrate, just throw it out completely and get new. i had that problem with the mites, that i just baked the substrate and i ended up getting more. also, if you think the flies might be on the crabs, try bathing them in a double concentration of IO. when i had the mites bad i did that, and only had to do one round of baths for the crabs, instead of stressing them out with lots.
i know you're not supposed to dig up crabs, but i really think this is an exception. definitely get an iso set up and get her out of there. i think it would be less stressful to be dug up then to get messed up by flies.
i hope you don't have to get rid of your little ones!

let us know how it goes, i'm hoping it works this time for you!