Thank you for the clarification
A chrooted environment is not a 
you will have to look more closely to the messages.
Originally posted by Jonathon, please see → Update or package installation returns “Failed to commit transaction (conflicting files); FILENAME exists in filesystem” (originating from pacman error: FILENAME exists in filesystem / Newbie Corner / Arch Linux Forums)
The big hammer - smashing all
pacman -Syu --overwrite '*'
I didn’t say it could not be done - what I said was/is - the scenario is unsupported.
Depending on the device it may run fine but it requires some special attention due to the nature of USB sticks e.g. grub maintenance and logging
Running of an always connected portable harddisk like the Samsung SSD does not equal running of a Kingston Datatraveler 64G USB stick. The underlying technology is not identical.