I did the same thing and had the same concern. I asked V&H about it. Answer if you flashed the Autotune it was saved. As I warned you FP3 software clears matrix each time you Apply Learned Values but the Learned Values are saved. Go back into Autotune selecting the same map that was flashed. Ride and continue to take screenshots. Compare to previous screenshots. See if new cells were learned. As I recommended make a matrix on paper to log green & yellow cells. Apply after each tank fill. Continue until you see no improvement then Finish the tune. ECM will be flash final tune. Then turnoff Autotune.
You will never get the entire matrix filled with green cells at 6000 rpm / 100% throttle. It takes a dyno tune to do that. But if you are able to tune to your normal riding condition it should be good. You will hardly ride above 5000 rpm / 80% throttle

 

Another recommendation is to view sensor data AFR table. It will show you the target AFR that was mapped

 

For some people it's also good to point out that the bike can run less than desirable when in auto tune mode until the finalization of the map is flashed.

 

I'm not sure what you are getting at here ...when? and to what end? Sounds as if the OP hasn't done much tuning so maybe a why and what you are looking for would be useful there. Setting up your AFR table from the rather basic V&H or Power Vision maps is a different tuning step and there are lots of which AFR table is best type threads and the OP can come back if stuck once he gets to that point.

I've never looked at AFR on the FP3 but target and measured can be useful when tuning with widebands and you are collecting data logs on the Power Vision for example?

 

There are a lot of videos you can watch to see how to do autotune, most of them are rubbish and do not explain everything.

Your original stock map is saved in slot 1.
The map you downloaded and flashed to the bike as part of the starting out process is in slot 2 (or wherever you put it)


When you start an autotune you tell it which map to use as the basis for the tune, so the one it downloaded would be the one to start with.

The auto tune process changes a whole pile of things, like reducing spark advance, switching off accel/decel enrich/enlean, etc and flashes this tweaked map into the ECU. So the engine is running a "modified" copy of the start map you picked.

Most importantly the auto tune process sets ALL of the cells in the AFR table to 14.3 so that the stock narrowband sensors can read how close the mixture is and that allows it to calculate what the new value for the VE table cells should be so that the ECU can calculate AFR values correctly.

When you have collected enough green cells you can then do something with what it has learned.

On the other hand, picking the Turn off Autotune option does exactly that ...give up, stop, quit, didn't want to do that, whatever.

Clicking Apply learned values gives two useful options......
Apply - flashes the newly learned VE values to the map that is programmed into the ECU, resets the hits screen back to empty and starts collecting data again.

This is relevant because once the cell is green, it will not learn any more! The point being, auto tune only adjusts VE values by a maximum amount ...so it may take more than one autotune to get it to the right value. This is why it is REALLY useful to see how much the VE values are changing between each auto tune session - get to within a 3% change and that is probably as good as it is going to get. Compare ALL the cells, especially the ones you maybe didn't manage to hit last time.

Finish - essentially takes the map you started the autotune with and changes the VE tables with whatever has been learned and than asks you to save this somewhere and flashes it to the bike.

On the hits screen, clicking the lightening symbol at the top right also does a Finish

So that you can compare how you are getting on, and to go back a step if one autotune session messes something up, I always save to a new slot.

I also always Finish rather than doing an Apply, for those same reasons. So...

Start autotune using downloaded map
Finish and save to new slot as AT1 (or make up your own name obviously)
Start autotune again using AT1
Finish and save to new slot as AT2
Start autotune again using AT2
etc
If you run out of slots, start overwriting the oldest ATx (so you always have your last 4 autotunes ...basically, don't overwrite something you want to keep e.g. you may have two tunes for two different exhausts?

There are some old ideas about running autotune for an hour or a tank of fuel, forget that! When that cell goes green it is not going to learn anything more. During autotune Adaptive Learning is disabled so running a tank of fuel is meaningless.

What is important is getting as many of those cells as possible to the point that any change by autotune is small. I can get most of the cells green within 20 minutes and if you can do that each time you should be done in 3 sessions or so.

Some people autotune the low load areas first a few times to get that dialled in, lots of around town and second gear launches for example, then pop out on the highway another day or whatever and do the higher load areas. Up to you how you want to tackle it.

 

It will get much easier and that Apply option may be more useful when we can see the percentage changes on the hits screen - that will instantly show where you might need to do a bit more work.

 

I think I am starting to understand! Thanks
Here is my first apply from this morning and the second apply from 20 minutes ago.

 

We do this because a large part of this column is also responsible for cold/hot start and idle. We did not want AutoTune to change these areas. It requires an entirely different procedure to accurately calibrate your idle and starting areas. Most setups that are intake and exhaust only do not have big enough VE changes to justify a change from stock.

 

So heres my last and final screen shot for my autotune. I have now selected finish and flashed the data to the ecm. So heres my last question. all three runs i varied my riding style city, hard pulls, highway. In the second image 1250 rpm at 10% throttle was learned. That map was saved. On the third and final run the same cell was not learned. Do the cells overwrite the previous data saved or does it see that it was already learned and saved and forget about it?

 

A new autotune will calculate new data for the cells it hits. If you click Apply, that puts the learned values into the ECU and starts again to collect new data.

The new number may be the same as the old number, or it may be a couple of point out, or it may be a significant change

This is why it is useful to Finish, save the new autotune map, run autotune again, Finish again and save that new map to a different slot. Then you can compare the two.

Autotune will only change a cell by 15% I think it was. So if your base map had a cell that was 80 but with your changes it now needs to be 108 ...that will take more than one autotune run to get.