What the Author Wrote, What the Agent Reads: Silent Cue Loss in Enterprise Document Ingestion

Yikai Zhao, Saurabh Pandey, Pradeep Kumar Misra

Enterprise agents act on documents. Before an agent can follow a policy, answer a compliance question or file a ticket, some ingestion layer must turn a Word file or PDF into tokens - and that layer is where an agent deployed in the wild silently loses information. We show that one layer is lost by every mainstream converter - the meaning an author encodes in how text looks - and that the loss makes agents confidently wrong rather than visibly incomplete. We build a task from 76 real policy documents: recover the requirements the author singled out, scored against the file's own OOXML properties by a deterministic matcher with no LLM judge. Formatting-blind ingestion collapses from micro F1 0.690 to 0.150 (docling) and 0.075 (plain text), a gap that replicates across six answering models from two vendors - five Claude models spanning the Opus, Sonnet and Haiku tiers, and OpenAI's GPT-5.6. An agent that cannot see the cue guesses, and docling's false-positive rate on requirements the author did not flag is four times ours. A span-level leave-one-out localises the loss to two cues - highlight (+0.302) and colour (+0.262), both Holm-adjusted p < 1e-4 - while bold, italic, monospace…