Adding fruits and veggies should not affect your gut flora in any way - if anything it would have helped fuel healthy bacteria (prebiotic foods). It's important you are adding in foods that supply the nutrients from the foods you are now avoiding.
While I am not quite sure what the issue may be, a couple thoughts that come to mind include: maybe you consumed too much at once...often when starting it's best to begin with a small portion (the small cup) and then work your way up. In addition, chia cause a get-like thick consistency which may have filled you up too much. Are you using organic produce - sometimes pesticides or residue on conventional produce causes allergic reactions in some. Is there an ingredient you are intolerant to or could there have been any type of food-borne bacteria on any of the produce you used?
I'm sorry to hear this and hope that your naturopath can help you determine the cause so you can Blast without hesitancy and reap the benefits. Keep me posted.