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I ran:
pacman -Syu
this morning and it destroyed my installation.
I got nowhere after trying to repair things, so I removed the entire folder.
I reinstalled MSYS2
I ran :
pacman -Syu
it destroyed the installation again.
So, pacman thinks your MSYS2 installation is a ghost and eats it.

Same or similar problem here. I got it running through a new installation, but when I try to compile commands like Make and Strip are not found anymore.

I filed a bug report and it is related to another bug.

There is a work-around. You can still update with
pacman -Syu
BUT you have to wait until all the background programs exit by themselves and it can take a long time.
To be sure, watch the processes with process monitor.
I imagine it will be fixed before long, but I have installed three times because of it.
The first time, because I did not know about it.
The second time because I wondered if it was fixed.
The third time because I wondered again.
But now I know what to do.