If you run the DMT Bill Of Operations Import in Delete mode and set the ECOOpDtl#RowMod field to D, this tells DMT that you want to delete the Scheduling Resource rather than the whole Operation.
E.g.
Company,ECOGroupID,PartNum,RevisionNum,AltMethod,OprSeq,OpCode,ECOOpDtl#OpDtlSeq,ECOOpDtl#RowMod
EPIC06,Eng1,001MP,A,10,NoHours,20,D