diff --git a/app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunSetup.tsx b/app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunSetup.tsx
index d54c223a8a5..3204293a7cc 100644
--- a/app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunSetup.tsx
+++ b/app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunSetup.tsx
@@ -1,4 +1,4 @@
-import { useState } from 'react'
+import { useEffect, useState } from 'react'
 import { useTranslation } from 'react-i18next'
 import { useDispatch, useSelector } from 'react-redux'
 
@@ -133,6 +133,13 @@ export function ProtocolRunSetup({
   const noLwOffsetsInRun =
     useSelector(selectTotalCountLocationSpecificOffsets(runId)) === 0 && isFlex
 
+  // A separate app can apply offsets. We need to update the missing steps as a side effect.
+  useEffect(() => {
+    if (flexOffsetsApplied) {
+      dispatch(updateRunSetupStepsComplete(runId, { [LPC_STEP_KEY]: true }))
+    }
+  }, [flexOffsetsApplied])
+
   const offsetsConfirmed = isFlex
     ? flexOffsetsApplied && !missingSteps.includes(LPC_STEP_KEY)
     : !missingSteps.includes(LPC_STEP_KEY)
@@ -266,9 +273,6 @@ export function ProtocolRunSetup({
         <SetupLabwarePositionCheck
           {...{ runId, robotName, robotType }}
           setOffsetsConfirmed={confirmed => {
-            dispatch(
-              updateRunSetupStepsComplete(runId, { [LPC_STEP_KEY]: confirmed })
-            )
             if (confirmed) {
               dispatch(appliedOffsetsToRun(runId))
 
diff --git a/app/src/organisms/Desktop/Devices/ProtocolRun/SetupLabwarePositionCheck/FlexSetupLPC/LPCSetupFlexBtns.tsx b/app/src/organisms/Desktop/Devices/ProtocolRun/SetupLabwarePositionCheck/FlexSetupLPC/LPCSetupFlexBtns.tsx
index c9fc8fa24ac..f22a4e78074 100644
--- a/app/src/organisms/Desktop/Devices/ProtocolRun/SetupLabwarePositionCheck/FlexSetupLPC/LPCSetupFlexBtns.tsx
+++ b/app/src/organisms/Desktop/Devices/ProtocolRun/SetupLabwarePositionCheck/FlexSetupLPC/LPCSetupFlexBtns.tsx
@@ -17,7 +17,6 @@ import {
 import { useToaster } from '/app/organisms/ToasterOven'
 import { useLPCDisabledReason } from '/app/resources/runs'
 import {
-  selectAreOffsetsApplied,
   selectIsAnyNecessaryDefaultOffsetMissing,
   selectLabwareOffsetsToAddToRun,
   selectTotalCountNonHardCodedLSOffsets,
@@ -31,6 +30,7 @@ export interface LPCSetupFlexBtnsProps extends SetupLabwarePositionCheckProps {
 
 export function LPCSetupFlexBtns({
   setOffsetsConfirmed,
+  offsetsConfirmed,
   launchLPC,
   runId,
   robotName,
@@ -41,7 +41,6 @@ export function LPCSetupFlexBtns({
   const isNecessaryDefaultOffsetMissing = useSelector(
     selectIsAnyNecessaryDefaultOffsetMissing(runId)
   )
-  const offsetsConfirmed = useSelector(selectAreOffsetsApplied(runId))
   const [runLPCTargetProps, runLPCTooltipProps] = useHoverTooltip({
     placement: TOOLTIP_BOTTOM,
   })
@@ -79,6 +78,16 @@ export function LPCSetupFlexBtns({
     }
   }
 
+  const runLPCDisabledTooltipText = (): string | null => {
+    if (lpcDisabledReason != null) {
+      return lpcDisabledReason
+    } else if (offsetsConfirmed) {
+      return t('offsets_already_applied')
+    } else {
+      return null
+    }
+  }
+
   const onApplyOffsets = (): void => {
     if (!isApplyOffsets && lwOffsetsForRun != null) {
       setIsApplyingOffsets(true)
@@ -103,12 +112,14 @@ export function LPCSetupFlexBtns({
         onClick={launchLPC}
         id="LabwareSetup_checkLabwarePositionsButton"
         {...runLPCTargetProps}
-        disabled={lpcDisabledReason !== null}
+        disabled={lpcDisabledReason !== null || offsetsConfirmed}
       >
         {t('run_labware_position_check')}
       </SecondaryButton>
-      {lpcDisabledReason !== null ? (
-        <Tooltip tooltipProps={runLPCTooltipProps}>{lpcDisabledReason}</Tooltip>
+      {lpcDisabledReason !== null || offsetsConfirmed ? (
+        <Tooltip tooltipProps={runLPCTooltipProps}>
+          {runLPCDisabledTooltipText()}
+        </Tooltip>
       ) : null}
       <PrimaryButton
         onClick={onApplyOffsets}