If you watch the EAF, you can see it counter-rotating a little each time it hits the hard limit -- and at the same time emitting the double beep. When you ask it to advance yet again, the action will repeat -- hits the stop, then counter rotating slightly, and emits a double beep again.
See if the flexible coupler is still rotating after the hard limit. If it does, check the grub screws at the OTA end. If the flexible shaft is not rotating, but the EAF indicates it is still moving past the hard limit, check the grub scrws at the EAF end.
I do see the counter-rotating slower as it gets close to its limit and then stops when it reaches its limit, even if the numbers continue to move. Therefore, I don't think it is stripped. I can't see the flexible coupler moving but I do hear a noise inside of the EAF once it hits the manual focuser limit, even if it has not reached the Max Step limit.
I just never get the double beep unless it gets to the max step limit.