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Pepper Maggots

I've come to the realization that I'm going to lose the bulk of my peppers this year, and it sucks. I had an opportunity to use a family member's empty garden this season, and quickly filled it up. In one of the rows, I planted the bulk of my pepper plants. Nothing fancy, just some hot cherries, tabasco, kung pao, butch TT, and chocolate habs. The cherries really took off first, and grew quite tall with lots of fruit. But every single pepper was hit by the pepper fly, which I guess are only common in southeastern New England. I had never even heard of these pests before, and now I have to open every pepper up and look inside for a maggot.

Since I want to try overwintering a few plants, I'm thinking about digging them up now and keeping them in big containers at my house, which is 50+ miles away. I've never had any problems with the pepper flies at my house, and I'm hoping that any peppers that form at my house will be unaffected, since the flies inject their eggs once the fruit has formed. At least I'll end the season with a few. And I'll remove all existing fruit from the plants before I transport them, to ensure that I don't bring the pests to my yard.

So is it a bad idea to dig up a flowering plant and keep it in a container? Will it cuase too much shock, even if I dig well beyond the root ball and dump it into a fresh batch of happy frog?
 
i would think it would still be possible to transfer the problem even after you remove the fruit. maybe not, but that's my thinking
 
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