in a similar situation I just identified the account with the correct license using the account subscriptions page online, and then signed out of all accounts in office at which point I believe it starts hounding you for an office license. Only then sign in again with the correct account. At this point you could ask them if anything is missing...
as for why this might be happening, my money is on there is some microsoft feature the end-user requires, eg skype, teams, onedrive etc, that is tied to another microsoft account of theirs (the one with the the Home & Student license) and when they sign in to that MS is applying the account to office as well, potentially they are clicking the "use this account everywhere" button which might make it supercede existing licenses...
maybe...
Having thought about it more, it probably won't be the case IF both these licenses are tied to the same MS account, but in that case I have always been asked which license to apply to office, never given the choice to use both...
as for why this might be happening, my money is on there is some microsoft feature the end-user requires, eg skype, teams, onedrive etc, that is tied to another microsoft account of theirs (the one with the the Home & Student license) and when they sign in to that MS is applying the account to office as well, potentially they are clicking the "use this account everywhere" button which might make it supercede existing licenses...
maybe...
Having thought about it more, it probably won't be the case IF both these licenses are tied to the same MS account, but in that case I have always been asked which license to apply to office, never given the choice to use both...
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