I have been exchanging emails with Wayne and sharing some of mine and Tom's experiences and results. As a result Wayne has released an updated version of TuneEdit v3.06 that now allows for the forced adaption of the ECU after a tune has been downloaded. This is basically the same as a the "12 minute tune." I have not tried it yet but Wayne said a check box will appear after a tune is loaded asking if you want to force adaptions or not.
We have found that after performing some significant changes to a tune and then returning to the previous tune that the bike did not perform quite like it did with the previous tune however after some time it would improve.
A word of caution though doing this each time after loading a tune may cause what changes you have made to the tune to react differently since you are changing the adaptions the ECU has made in relation to your riding habits, altitude etc. Think of it as not forcing adaptions but wiping the slate clean so new adaptions can be made. Therefore a different baseline might be present. For more info see page 11.133 in the Triumph Rocket III Service Manual.
A good rule of thumb would be to use this feature after making air filter, air box, and exhaust mods. Also after running a tune that caused the bike to run poorly when you plan to return to a previous tune for an extended period of time.
Also in the latest version are the means to change the rev limiter in the tune constants. This ability came with a word of caution from Wayne stating that raising it could cause the engine to run lean in that RPM range because the fuel maps are targeted to the stock limit and the fact that the secondaries would be fully closed at that point.