I'm sorry to hear of your loss. While flies cannot be totally eliminated, there are steps one can take to prevent maggot infestation in the future. The first, is checking the rabbits daily for signs of these. A flea comb is helpful You can read more here: http://www.rabbit.org/journal/4-3/house-fly.html As for controlling flies in your environmnet, change their bedding frequently, remove items that may drawn flies (for instance, if a compost pile is nearby) and speak to an extermator about eco-friendly pesticides. More can be read here: http://www.rabbit.org/journal/2-12/fly-strike.html Again, I'm sorry to hear that rabbit passed and hope the above is helpful to you.
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Thank you very much for the information.