A/R gets messy after an EHR switch because old balances, payments, and claims rarely move over cleanly, and the connections that carry claims and payments between you and your payers have to be rebuilt. The fix is to keep the old system running long enough to finish its own claims, pull the right reports before you lose access, work old balances in order of their filing deadlines, and reconcile your bank deposits against what's actually posted.
I've spent 15+ years in medical practice management, from the front desk to billing management. A system change is one of the easiest times for revenue to slip through the cracks, usually not because anyone did anything wrong, but because for a few months nobody is sure which system owns which claim.
Why A/R gets messy after a system switch
Migrations are built mostly to move patients, schedules, and clinical records. Billing history often comes across incomplete. The usual trouble spots:
- Open balances that didn't migrate, or came over as a lump sum. Insurance balances are often left behind entirely. Patient balances may arrive as a single "balance forward" amount with no claim or date of service behind it.
- Unapplied payments and credits. Money that was never matched to a claim in the old system doesn't sort itself out in the new one.
- ERA and EFT enrollment gaps. Electronic remittances (ERAs) have to be enrolled to route to the new system, and many payers send them to only one destination at a time. EFT deposits are tied to your bank account, so they usually keep coming. That's how you end up with money in the bank and no explanation of what it paid for.
- Clearinghouse re-enrollment. If your new system uses a different clearinghouse, some payers require a new enrollment before they'll accept claims or send remittances through it.
- Payer ID and submitter ID changes. A payer ID you've used for years may differ at the new clearinghouse, and payers that assign submitter or trading partner IDs need the new one linked to your practice.
- Duplicate patient accounts. A migrated patient who gets re-registered at the front desk ends up with two accounts, and payments land on the wrong one.
- Claims stuck between systems. Visits near the cutover can get billed twice, or not at all, because each side assumed the other had them.
- Rejections nobody is watching. The old clearinghouse stops getting checked, and the new rejection queue isn't on anyone's daily list yet.
Run both systems in parallel for a while
The simplest rule I know is to pick a cutover date by date of service. Everything before that date stays in the old system until it's paid, finally denied, or written off. Everything on or after it goes in the new one.
Rule of thumb: don't move open claims between systems. Recreating an old claim in the new system to "get it out the door" is how duplicate claims and double-posted payments happen.
Keep the old system, and ideally its clearinghouse connection, active long enough to post payments, work denials, and send corrected claims for those older dates. Check your agreement with the old vendor for how long you'll keep access and whether it turns read-only. Read-only is fine for lookups, but you can't post a payment or close out a claim with it.
Once ERAs route to the new system, remittances for old claims will land there with nothing to match. Someone has to post them by hand in the old system, so decide now who that is.
Reports to pull before you lose access
Before the old system goes away or goes read-only, export these and store them securely, like any other PHI:
- A/R aging by payer and by date of service, for both insurance and patient balances
- Every open claim with claim-level detail: patient, date of service, codes, billed amount, payer, submission date, and current status
- Unapplied and unposted payments, plus credit balances
- Denial and rejection reports, including anything still sitting in a work queue
- Patient balances, statement history, and any payment plans
- Payment history by deposit date, for reconciliation later
- Clearinghouse acceptance reports for submitted claims
That last one is easy to forget, and those reports are often your best proof of timely filing if a payer says it never received a claim. Save everything in a format you can open without the old software, like a spreadsheet or PDF.
Triage old A/R before timely filing runs out
Once you have the open claims list, the first question isn't "which claim is biggest?" It's "which deadline is closest?"
Medicare's timely filing limit is 12 months (one calendar year) from the date of service. Commercial limits vary by contract, often 90 to 180 days and sometimes shorter. Medicaid programs and their managed care plans set their own limits too. Check each contract instead of assuming one number covers everyone.
A simple order of operations
- Add a "file by" date to every open claim based on that payer's limit.
- Separate rejections from denials. A rejected claim never made it into the payer's claim system, so it doesn't count as filed, and the clock is still running.
- Work the claims closest to their deadline first, starting with the larger balances in that group.
- Move on to denials with appeal deadlines. Appeal and corrected claim deadlines are separate from the original filing limit and can be shorter.
- Chase claims with no response. A call or portal check tells you whether the payer even has them.
- Bill patients after insurance is settled. Hold statements on visits with an open insurance claim, so you aren't billing for amounts a payer may still cover.
Some claims will turn out to be past the limit. Before writing them off, look for proof of timely filing and ask about a reconsideration process. Before billing a patient for a claim denied as late, check your contract. Many in-network agreements don't allow it.
Reconcile deposits against posted payments
This tells you whether the money is where your reports say it is. I'd do it weekly for the first few months after cutover, then at least monthly. Compare:
- What landed in the bank, including EFT deposits and checks
- What was posted in the old system and the new system combined
Each EFT deposit should match a remittance, usually by the EFT trace number on the ERA. If it doesn't show on your bank statement, ask your bank how to see it. A deposit with no matching remittance often means an ERA went to the wrong place or was never enrolled.
If posted payments come up short of deposits, you have unposted money. If they come up higher, something was likely posted twice, often once in each system. Either way, it's far easier to sort out within the month than a year later.
When to bring in help
A system switch lands on top of training, new workflows, and a full schedule, and old A/R is usually the first thing to slide. It may be time to get help if:
- The aging report in your new system doesn't make sense, and no one can explain why
- Deposits and posted payments don't match, month after month
- Access to the old system ends soon and the open claims list is still long
- No one owns the rejection queue in either system
- Your biller left in the middle of the switch (start with what to do when your biller quits)
- You're changing billing companies at the same time (here's how to switch billing companies without losing revenue)
A/R cleanup is part of what I do at S2S Medical Billing Co., where we work primarily with behavioral health and PT/OT practices. That includes working old claims to closure, reconciling deposits, and fixing ERA, EFT, and payer enrollments through our credentialing and payer enrollment service. You can bring us in for the cleanup alone, or for ongoing billing afterward.
We sign a Business Associate Agreement before any patient data is shared, ongoing billing is a flat monthly retainer plus a per-claim fee (never a percentage of collections), while A/R cleanup is billed hourly; see pricing, and you work directly with me.
If you've just switched systems, or you're about to, and aren't sure what's sitting in your old A/R, reach out. Tell me where things stand, and I'll help you figure out what to tackle first.
