A system and method are provided for recovering from print assembly failure in a printer with printed medium assembly capabilities. The method generates a first print set including a plurality of physical medium sheets, and stores the first print set of a first interim stacker. A second print set is generated including a plurality of physical medium sheets. Sheets are accessed sheets from the first interim stacker and assembled with sheets from the second print set, generating a final print set with a plurality of sheets in a first order. The final print set is stored in an output stacker. In the event of a first print set failure, first print set replacement sheets are generating. In one aspect, generating the final print set includes directly merging first print set replacement sheets (bypassing the interim stacker) with sheets from the second print set.