Panacur might be safe enough to administer to gravid females, but Flagyl has more of a risk factor. Is your gravid female showing any symptoms? Has she come into contact with the other leos? You may want to get a fecal test done for her just to confirm if she's carrying anything. Flagyl is used to treat bacterial and protozoal infections (not worms), and both can cause problems when her body is going through the stress of egg-laying.
I'm also wondering about the dosage of Flagyl that was prescribed. With herps, it's normally administered once, with a follow-up in 3-4 days. That would mean a larger dosage each time you administer it, but it's less stressful on the geckos.
How fresh were the samples you brought to the vet? You have to make sure the poop doesn't dry out, or else it won't do you any good. When you have a sample, seal it up in a Ziploc bag, maybe stick it in a little empty yogurt container (for sanitary reasons), and keep it in the fridge. Aim to get the sample tested within 24 hours of it being pooped.
Anyway, it just sounds like your vet is trying to get all the bases covered. It's better to know for sure that crypto isn't the problem than to wonder about it. Nothing wrong with that. If I were you, I'd see if the leos respond to the Flagyl treatment first. If they don't show improvement, then that's when you may want to test for crypto.
In my opinion it's not necessary to utilize UV, but it would help to increase the temperature of the enclosure. Bump up the warm side to the lower 90s, but make sure they're able to hide all along the thermal gradient. Make sure they feel secure as well. Stress will only work against their immune system.
And last but not least, you should keep them on paper towels so that you can replace the substrate every time they poop. You have to make sure to keep their cages clean so they don't re-infect themselves during treatment.
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chickabowwow
