Mate, that's unfortunate and I sympathise with your loss of $$$ but why on earth did you bother with the on-line 'comparing' agents? Where did the paperwork say you had to get the cheapest ticket from a bucket shop?
When you are asked to get your own ticket you are asked to use ANA if possible. You said you had to make a connection in order to do this, so why didn't you find the return ticket to the ANA-served airport and just book both using the direct websites, instead of flylatebutcheap.com? You'd get the money back and nowhere do they ask you to move heaven and earth to get here, just buy an economy ticket. You may well have been able to use the direct flight offered by your current employer but did you ask? I was allowed to do that, even though ANA had a direct flight too
In summary, they are not asking you to do anything but book your own economy ticket and use ANA is possible. No need for cheapo websites because you're going to get your money back, so it's not your pocket you're dipping into. It is, however, an important lesson to us all how anally retentive the Japanese are when it comes to following the letter, to the letter. Individual thought, common sense and initiative is not allowed in Japan. They are robots and you, too, must be a robot whilst working for them. This = follow what is written and not use your brain to get it cheaper for them/you
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