Update on this, now we've solved it through a support case. The method of updating the config.properties so that
mdb.undeploy.deletedata = true
is set clears out -all- data usm_* MDB tables (though not the tables themselves). However, this means that the re-install gets confused - the MDB is partially there, but it can't tell the version. We ran the following SQL query to tell it:
insert into USM_SCHEMA_VERSION values (14, 1, 0)
Now it knows that the table schema is for a 14.1 system with no patches. You can then run through the reinstall, and the content section will correctly reload it.
thanks
Iain