FWIW, I had separate tunes for 91 and e85. I switched back and forth a handful of times and never had an issue. When I went from 91 to e85, I would usually run rich for a short period until the fuel trims adjusted. Conversely, when I went from e85 to 91, I had a brief period where things were a little on the lean side but within perhaps 20-30 minutes of driving, the fuel trims adjusted again and compensated.
I normally drove the car with a lighter right foot for awhile after switching fuels until AFRs stabilized but it was never a big deal. I would say as a general rule it's wise to run out as much of the old fuel as you can, then when you do re-fuel and re-flash, just drive moderately until you see your fuel trim and AFRs back in line.