I've managed to separate the entries. The original tags appear on the epub's titlepage. However, the prefixed copies aren't being added to Calibre for some reason.
I did something like this:
Code:
[archiveofourown.org]
add_to_valid_entries:,prefix_ships,prefix_category,prefix_rating,prefix_status
include_in_prefix_ships:ships
include_in_prefix_category:category
include_in_prefix_rating:rating
include_in_prefix_status:status
replace_metadata:
# other regex I do for cleaning up the tags
prefix_ships: other stuff
# then I put the prefix last, can't tell if this expression is correct since it won't show up in Calibre's tag database.
prefix_ships=>(.*)=>p\: \1
include_subject_tags: prefix_ships,prefix_category,prefix_rating,prefix_status