Considering you mention later you have two disks, i suppose you mean to have Windows on a disk with MBR, and Manjaro on the other with GPT. This is entirely feasible.
Here GPT and MBR are about disk partition tables. There is only one such table per disk (hence the name), and each disk uses its own. So you can very well have multiple disks, mixing MBR and GPT.
You may confuse this with MBR and EFI, in the sense of boot loading. Those are different methods of staring and booting entries for operating systems, and usually can’t be mixed without issues.
On a side note, there have also been numerous reports of Windows updates overriding the boot loader. Though your situation does seem more complicated.
Well, there are many occurrences of that discussed here, usually because of a kept unsupported kernel.
More than not what is “usually” does, rather definitely not what it can do: mhwd is a utility for managing specific packages, namely kernels and drivers. I highly doubt you lost all your data because of it.
Have you checked your drives’ health? If the file system begins behaving erratically, this is usually a sign of drive failure…
Please also provide information about your system.