2005 Mustang GT Failsafe Mode questions

I got to experience the wonderful FailSafe mode the other day. I was switching tunes over from 93 to the 87 Economy tune on my SCT X3. I drove the car down to "0 miles till E" before putting in 87.

I fill her up about halfway, load the tune at the gas station and head out, as I'm going down the street the car jerks and goes into Failsafe. My first thought was that the gas left in the injectors and fuel lines was the 93 and threw the car for a loop.

After idling for a bit, and then reloading the tune, it still did it. I then went back into the SCT and found my problem. Apparently it wasn't the gas at all. The settings for the 87 Economy tune still had the stock airbox saved, not the C&L. My 93 performance and economy tunes both have the C&L Racer saved and since I haven't used the 87 since installing the CAI I forgot to update those settings. So needless to say, changed the airbox setting and reloaded the tune, good to go, no more failsafe.

I am curious though, does failsafe do any damage to the engine? I know it prevents damage, but does it cause issues? How long should you drive around in failsafe mode?