Quote form another thread, which discussed using same external hard drive for Windows and Linux:
This I take to mean that Duplicati is not desgined so that the local databases can be used across different types of operating systems. You can use databases created on Linux on other Linux distros, you can use databases created on Windows on other versions of Windows, but you cannot mix.
I am not sure if the same principle also pertains to the backup files on the target file system, though. You can try, but be extra careful to use test data, so you do not destroy any valuable data.
EDIT: Note that if your test succeeds, you can recreate the local databases beforehand, before the hostwap. You just initiate a restore operation that does it for you. I cannot remember how to do it without actually restoring any files, but I’m sure it is possible.
But then, again, in order to test your scenario (restoring to another platform), you do have to attempt an actual restore from your live target to Linux. Whether the database that results from your test run can be used in the actual hotswap depends on timing.