If the relationships were reaped (or deleted) as would be expected after a dataset destroy operation then they must be rebaselined. Importing them into a new dataset only will work if the relationships were not reaped, and even then the ability for UM to grow the secondary location would be lost.
Assuming that the dataset was restored using the database backup (all or nothing restore - all data collected or generated after the backup creation would be lost in the restore), the relationships would still need to be recreated on the controller side.
I assume you are talking about protection manager here. To correct this issue recreate the dataset as a new one with no members. Once the settings have been restored you can simply import the relationships into the dataset.