I suspect that your beardie is reinfecting itself rather than the coccidia becoming resistant. It is very easy for them to become reinfected. You have to be hypervigilant about cleaning their environment during treatment. I personally use Nolvasan for the enclosure and a dilute Nolvasan solution top soak feet, tummies and tails that come in contact with diarrhea. I use a 10% bleach solution for cage furniture. Make sure if you use a sand substrate (or other "loose" type substrate) you remove it and use paper towels or shelf liner (the forum rec. Duck brand from Walmart, cheap to replace). Anything can harbor coccidia and potentially reinfect your beardie.
In response to the previous response, Are your beardies sick with cocidia? What symptoms do they have? Coccidia are commensal oirganisms in beardies, but they can easily cause an opportunistic infection in response to stress, illness, etc. What kind of numbers is your vet seeing? (Usually expressed in number of ova per high power field).
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Stacey