I just double-checked that with the current firmware [1.3.0 (Build: 2711)] this does not happen here.
If I choose to ignore the second call, it ultimately goes to voicemail.
If I press the FLASH button on the phone, the original call is placed on hold and the second call is answered. Additional presses of the FLASH button alternates between to two calls.
If you're losing the first call when you press the FLASH button to answer the second call, it may be that your phone produces an abnormally long on-hook time and you need to increase:
Physical Interfaces -> PHONE Port -> HookFlashTimeMax
to prevent the OBi from interpreting the FLASH button as a hang up.