I know this is an old post but I registered here to follow up on this, cause I was having the same issues, and couldnt find any info online to help.
I recently bought an eflite apprentice (with "SAFE"), and was also having issues entering the esc programming mode. I narrowed it down to a conflict with the SAFE receiver initializing while the esc is powering on (when it should be entering programming mode). I assumed the SAFE system initialization is interrupting the "full throttle" input.
I figured out how to work around this by doing the steps below. I dont have another receiver without SAFE to use for programming the esc, which would be easier than my work around....
1) REMOVE YOUR PROP FOR SAFETY, lost digits make it hard to fly
2) You will need another battery (6v NiMH or some other way to power the receiver for programming the esc). By default, the apprentice receiver is powered off the lipo / esc, and the receiver is powered via the "throttle" plug (red wire) on the receiver. However you can, instead, power the receiver via the "bind" port, to initialize the SAFE system before the ESC is powered on, allowing you to enter the esc programming mode. You do NOT want to power it by both batteries though, you'll fry your receiver.
3) Unplug the throttle JST connector from the receiver (the wires coming from your esc to the receiver)
4) On the back of the JST connector you will see the 3 metal pins, they are held in place by a small plastic "tab" that can carefully be lifted (there is 1 tab per pin) with small flat screwdriver to release the pin. You only need to lift the middle (red wire) plastic tab to release the red wire pin. Be careful not to break the plastic tab, you only need to lift it slightly to release the pin, this way you can reinstall the red wire pin when done.
5) Once the red wire pin has been removed, tuck the red wire out of the way so it doesn't short on anything (tape it off for safety), now plug the throttle esc JST connector back into your receiver. (pay attention that its plugged in correctly)
6) Turn on your transmitter that is bound to this receiver, set the throttle to 0 / full down
7) Plugin your 6 volt receiver battery pack to the "bind" port on the receiver (pay special attention to the + and - wiring to make sure its plugged in correctly). The receiver should now power on.
8) After the SAFE system initializes (servos will move on their own etc), you are ready to power up the esc and enter programming mode
9) Set your transmitter to full throttle, then plugin your lipo battery to your esc. Your esc should initialize, and enter programming mode. (for programming instructions, see the esc documentation that came with your apprentice, or find it online from eflite)
10) Once you are done programming your esc you can unplug your lipo battery, and your 6v receiver battery. Remove your "throttle" wire from the receiver again, and simply slide the red wire back into the middle port of the JST connector and ensure it remains secure. Plug the esc JST wire back into your receiver (again making sure to plug it in correctly) and you should be back to "stock".
I searched the internet high and low trying to figure out why I couldnt program my apprentices esc, there is no information about the SAFE system interfering with getting the esc into programming mode, but it is. The above worked for me, hopefully it'll help someone else out that is searching like I was.
The reason why I wanted to reprogram my apprentice's esc was because it was low on power / thrust. The very first flight off the ground it felt fine, but after landing once - the motor cut out ~4 times on the ground when giving it part throttle - as if it was hitting low voltage cut off. I changed the battery and the bahavior remained, then suddenly stopped. Its been flying fine since, just low on power.
I've now upped my esc timing from the default of 15 degrees to 25 degrees in hopes of gaining back a bit more power, but I suspect the motor is somehow damaged (despite no hard landings). Bench running the motor at 25 degrees timing looks promising however, but I havent flown it yet - so we'll see! Its possible that my esc wasnt set to 15 degrees either (maybe the previous motor cut out issue zapped the esc programming?), but I was definitely lacking power with whatever timing my esc was set to. Now that its reprogrammed Im hoping to have a bit more thrust to fly with. it felt like I had only ~50% thrust of what I should, and sometimes I was barely getting off the ground (batteries etc all check out), climb performance is weak too.
Ive also already ordered a eflite power 25 1250kv & eflite 60 amp receiver, so if my thrust isnt restored, those will be going in soon anyway