Rotating Cipro and Flagyl *does* mean alternating them. Combination therapy (taking both at once) should be reserved for special circumstances, such as when either drug alone has proven ineffective. I’m on both, and they work great for me, but I only do this because they no longer work individually. Taking both at once can make it hard to figure out what to do if a troubling side effect occurs.
Cipro just has to be separated from dairy by a few hours. Through experimentation I found that my (fairly low) Cipro dose works just as well once daily as when it’s split into two doses. I take it at bedtime, well separated from my yogurt/VSL mixture.
Is this a new doctor for you? Have your symptoms gotten worse or changed? Is there any reason a more aggressive approach might be needed?