I think you have two options. If these are clients you had prior to 2018 then the easiest approach may be to delete the 2018 files altogether for this husband and wife. Then just carryforward the 2017 data to start the process all over again and just autofill once for either spouse. Note that CRA automatically identifies both applicable SIN accounts and autofills both.
If that is not a useful approach, then you'd have to go into each slip module and delete the duplicate entry for T4s, T5s, etc. Pay particular attention to the RRSP file to make sure that the annual limits have not been changed and that extra premiums have not been included by the autofill process.
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