I never heard about channel mapping on LE. You had a working system before your microSD died, so I think it's not a driver issue.
Because you have another HiFIBerry card, we can rule out a HiFiBerry firmware issue.
On the other hand, the RPi has it's own firmware, too. LE installs the right firmware, but maybe something broke while your microSD died.
My suggestion: Take another microSD, install Raspbian, and if Raspbian also has channel issues, try different RPi firmware on Raspbian.