I figured updating this might help someone sometime.

Creating the replication agent job manually didn't work. The job itself could be executed, but it didn't do anything and didn't result in the subscription reappearing in the Replication Monitor list. In the end, we had to drop and recreate the subscription, then manually edit the publisher sysmergesubscriptions record from the subscriber version of this table using this script:

update b

set recgen = a.sentgen

, recguid = a.sentguid

, sentgen = a.recgen

, sentguid = a.recguid

, status = 1

from <MySubscriberServer>.<MyDBName>.dbo.sysmergesubscriptions a

join sysmergesubscriptions b

on a.pubid = b.pubid

where a.pubid like 'B%' -- only relevant for my circumstances - use suitable criteria to limit to your publication

and a.subscriber_server = '<MyPublisherServer>'

and b.subscriber_server = '<MySubscriberServer>';

update b

set schemaversion = a.schemaversion

, replicastate = a.replicastate

from <MySubscriberServer>.<MyDBName>.dbo.sysmergesubscriptions a

join sysmergesubscriptions b

on a.pubid = b.pubid

where a.pubid LIKE 'B%' -- only relevant for my circumstances - use suitable criteria to limit to your publication

and a.subscriber_server = '<MySubscriberServer>'

and b.subscriber_server = '<MySubscriberServer>';

Obviously, this relies on having your subscriber server set up as a linked server on your publishing server.

This allowed the subscription to be synchronised normally. Incidentally, this approach can also be used to unmark a subscription that has been marked for reinitialisation.

Edit: typo

Edit2: removed database name