Archive files

The archive files present in ~/.unison are important and represent the database of the last synchronized state.
The name of the archive file is computed from the hostname of the computer that will run the Unison process, and from the path of the root (apparently it may also include a device node ID, not sure about this). This means that with the same paths but on different hosts, the archive files will be different. You can use the UNISONLOCALHOSTNAME to change the hostname, but you must remember to set it each time you run Unison.
The rootalias command can also be used to workaround this hostname component for the archive file name hash. However, there is currently a bug (https://github.com/bcpierce00/unison/issues/1131) and the slashes are not sanitized properly. You can still use rootalias, but the name computed will be different than if it were just ran with UNISONLOCALHOSTNAME set to whatever you choose for the hostname to the right of rootalias.

Debugging

Running with -debug verbose will output a lot of useful debug information, in particular it will show you how the archive file name is hashed from a source string.
You can use this to see which archive file belongs to which root (difficult to tell without this).