An intriguing concept, but needs tightening as a logline. ATM there is no protagonist and no goal -- two essentials for a logline. By opening with "after two boys disappear from..." means you are creating perspective from someone else other than the two boys (whom I'm assuming are your intended protags...". You should pick ONE hero and write from their POV (obviously just an example...):
"When attempting to go AWOL, a cowardly air force pilot stumbles across a secret government experiment that sends him back in time to the battle of Britain, and his only way home is to find a legendary pilot who's been lost for 50 years..."
Lastly, 'boys' seems odd... I'm imagining 12 and under... What would two 'boys' be doing at an air force base?
Anyway, best of luck.