Eu encontrei o mesmo problema, a sugestão de Darko_65 em Fórum de Respostas da Microsoft é o que funcionou para mim:
"bootrec" command sometimes has problems finding proper boot device and windows installation to fix.
Use "bcdboot" command to fix boot (bcdboot requires that partitions are specified explicitly!)
bcdboot C:\windows /s S:
specifies C: as Windows partition, S: as system partition.
Use "diskpart" or "mountvol" commands to map system partition.