A good way to tag files based on an external directory?

I have my mobile devices using a subsection of my library using beet-alternatives. With some files I also had manually added to the device directory.
And I need to find a way to add beets tags to each files of the files that are in the library and the external directory.

For example, if I have to rebuild my library from scratch. And afterwards I want to tag the relevant files so that beets alternates can rebuild a copy of the external directory.
Ideally there would also be a method to tag files that are duplicates of files that I had manually copied there.

I couldn’t find an easy way to do that.
Importing the files with --set mobile=1 would not work, because they would be duplicates that I don’t want to overwrite because they are converted down or are only album fragments. I suppose if I am mistaken and beets writes the tags even if you skip from the overwrite screen that might help.