I have gone through this and already fixed mine Mine i created another user, to see if same issues would occur in new profile, then open default file manager with dual window get it to show all files in directory access the configuration files in the other profile, look at all files, the structure, which directories are where and so forth. Then I went into my profile and remove all the hidden default directories. and any other non existing software that was no longer installed on my computer system. (I cleaned my system manually) After that I just rebooted my system, then re-logging back into my profile. after that is just re-linking all the software that i wanted to load. My Cinnamon changed back to the proper interface.
Assuming you are using a plain default Manjaro Cinnamon desktop (un-customized - no incompatibled applets and widgets).
For the sake of testing your issue, I did a clean installation on my Clevo w141u laptop - a test system for installations and updates.
I used the Cinnamon as it is available from manjaro web site.
The installation was flawless - wiped the disk - it is a test box.
Reboot and run pamac update - yet another reason I tested - other forum topics claiming pamac breaks mid-update - nothing of the kind - flawless update and after reboot the desktop environment is the same.
Just my 2 cents here, I have multiple DeLinuxCo installations, and of course they are all Cinnamon DE. I did have one system where Pamac crashed, waited a while, rebooted and all was good. The other machines, no issues at all. So it does not sound like a Pamac issue, might be, could be, but I don’t see it.