The honest EHR-migration data-loss checklist

The pre-migration checklist most vendors hand you is templated and reassuring. This one is about what actually goes wrong: the discrete data that quietly becomes a scanned PDF, the allergy whose "refuted" status flips to active, the lab feed that silently never reconnects. Every failure mode is anchored to the real HL7/FHIR, ONC, HIPAA, and code-system standard that governs it.

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Lead with this: Losing the code-system `system` URI is silent semantic loss even when the value looks intact — reconcile coded elements WITH their terminology binding, not just the visible code/display text.

General IT / operational guidance — not medical, legal, or compliance advice. This is a data-integrity validation checklist for EHR migration. Standards and versions revise; verify every citation and version against the live owner page and confirm requirements with your EHR vendor and your organization's compliance/HIM team before acting.

The seven silent-data-loss failure modes

Structured → unstructured loss

High-risk silent loss

Discrete, coded fields (labs, meds, problems) get migrated as scanned PDFs or free text — the values look present but become unqueryable and uncomputable. This …

Code-system mapping gaps

High-risk silent loss

Crosswalking SNOMED CT, ICD-10-CM, RxNorm, LOINC, and CVX between EHRs is where meaning silently shifts: version drift, one-to-many ambiguity, RXCUI≠NDC, retire…

Allergy & problem-list granularity loss

High-risk silent loss

Status and granularity fields default-flatten during migration. A refuted or entered-in-error allergy arriving as 'active', or a resolved problem reappearing as…

Dropped HL7 v2 / FHIR interface feeds

High-risk silent loss

Lab (ORU), registration (ADT), radiology, and pharmacy interfaces silently aren't reconnected after cutover — the classic migration failure where the data stops…

Attachment / scanned-document loss

Medium-risk silent loss

Document metadata migrates but the binary doesn't: broken or relative `attachment.url` pointers are the classic silent loss. For C-CDA, teams keep the human-rea…

Audit-trail / access-log loss

Medium-risk silent loss

Legacy access histories and audit logs are dropped at cutover — but the HIPAA 6-year retention obligation follows the DATA, not the system. You must still be ab…

USCDI / C-CDA portability completeness

High-risk silent loss

Use the cert-named US Core / USCDI version as the minimum completeness checklist. Anything in USCDI that doesn't round-trip is, by definition, silent loss of po…

By EHR

Epic Cerner / Oracle Health athenahealth Allscripts / Veradigm eClinicalWorks NextGen Practice Fusion

Why this exists. A practitioner on r/healthIT asked for "a more honest pre-migration checklist than the templated one everyone hands out." This is that — accuracy over breadth, with citations you can verify, not vendor reassurance.

Not medical advice. IT/operational guidance for EHR data-migration validation, anchored to official HL7/FHIR, ONC/ASTP, HIPAA (eCFR), and code-system sources. Last verified 2026-06-22. Verify versions and requirements with your vendor and compliance team. Some outbound links may be referral links.