(2020) Japanese bandplan includes 6m.
Not sure if you have put one of your 7000 boards inside a Japanese 7000 permanently but there is a diode matrix in the 7000 just like most modern transceivers so you might want to check which diodes are there and which are not.
People tend to generalise calling boards 'the logic board' so I'm not really sure what you changed.
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I bought a new 7300 from Japan recently and the only gaps in coverage compared to UK bands were in the 80m and 40m bands. All the rest were the same including full 6m to 54Mhz. It was easy to change diodes on the matrix to bring it to UK spec.
I don't think I would jump to suspecting something became corrupted and would check the matrix and connections first.
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rgds
Tony deG7WHK
Tony T