Home button not working but Touch ID does

Logically, you would expect the Home button action to work if the Touch ID works. The usual question is normally the opposite situation.

In your case, there could still be damage on the extension flex that runs beneath the backlight shield. Just think of it as a highway with multiple lanes. If the Home button lanes are damaged but the others are not, then you would see similar symptoms. You should inspect it closely and test continuity on each pin to be certain.

The other possibility is in how you are re-assembling the home button, specifically the backplate (iPhone 6 Plus Home Button Assembly Replacement). this is what the "button" presses against. If it isn;t making solid contact, the the button press will not be noticed.