Thread follow up, just in case anyone else has similar issues.
So flubendazole seemed to work really well - all the fish recovered, and have been fine. Unfortunately two are currently coming down with symptoms again. Do I really need to repeat the dose monthly? Catching the shrimp and moving them to a backup tank every month is going to be a nightmare.
One of the fish that isn't eating has a little bump in her belly, when I saw this last year the fish ended up dying after around two weeks, so hopefully another treatment will head that off. It's just very demoralising to constantly be going through this, let alone the impact on the aquarium inhabitants.