2 octane maps on stock ecu

Is it possible to use the high/low octane maps for the purposes of running say q16 or e85 on the primary map and using the low octane map for 93/91 pump gas? Given these maps are tuned relatively conservatively. Or should a completely separate map be developed for the different fuels?

You wouldn't be able to do this without recoding how the factory ECU works. While you haven't specifically stated what platform you're tuning on, in most cases the high and low octane tables are referenced depending on feedback from the knock control system. Changing to a fuel with dramatically different characteristics like E85 would also be problematic as we need to make some significant changes to aspects such as the stoichiometric ratio at a minimum in order to have the engine running correctly.

I was curious. I have an audi running eurodyne flashing software which has the ability to switch between octane maps by unplugging the maf. Wasn't sure if this forced the factory ecu into a low octane map which may have been setup to run a high octane fuel. But I know some vehicles will switch to an alpha n or speed density when the maf malfunctions. Wasn't sure if the would be applicable to open source software such as ecuflash. I figured the specific mass of the different fuels will require different afr's... So I would be more inclined to switch between e85 and c85 or 93 and 110 or along those line. Basically switching between similarly based fuels.

I'm not familiar with the eurodyne platform but what you're describing sounds feasible assuming that the ECU doesn't do anything funky. It's probable that the ECU will revert to the low octane maps as a precaution if the MAf is deemed to have failed but that is just my assumption. The thing you'd need to be careful of is if the ECU still continues to reference between the high and low octane maps under normal operation with the MAF functioning in response to knock. This could be problematic if you're trying to use these maps for a different reason.

With E85 we actually find the engine responds to similar lambda targets that we would use with pump gas, however we need to supply around 35-40% more fuel in order to achieve this target. This requires either the ability to change the fuel density and stoichiometric AFR with respect to ethanol content, or if the ECU doesn't provide any parameters for fuel characteristics then it's common to fudge the injector flow data instead. This would be difficult to do on an ECU that isn't set up for flex fuel from the manufacturer.