diff --git a/packages/cli/CHANGELOG.md b/packages/cli/CHANGELOG.md
index 99ccbabf0..98b6bf472 100644
--- a/packages/cli/CHANGELOG.md
+++ b/packages/cli/CHANGELOG.md
@@ -1,5 +1,12 @@
 # @openfn/cli
 
+## 1.38.1
+
+### Patch Changes
+
+- Updated dependencies [97dabc4]
+  - @openfn/deploy@0.13.1
+
 ## 1.38.0
 
 ### Minor Changes
diff --git a/packages/cli/package.json b/packages/cli/package.json
index 1ba4d5a0d..ade33cf32 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@openfn/cli",
-  "version": "1.38.0",
+  "version": "1.38.1",
   "description": "CLI devtools for the OpenFn toolchain",
   "engines": {
     "node": ">=18",
diff --git a/packages/deploy/CHANGELOG.md b/packages/deploy/CHANGELOG.md
index bdc72b1fc..c3996736a 100644
--- a/packages/deploy/CHANGELOG.md
+++ b/packages/deploy/CHANGELOG.md
@@ -1,5 +1,11 @@
 # @openfn/deploy
 
+## 0.13.1
+
+### Patch Changes
+
+- 97dabc4: Ensure that workflows can be removed in v1 sync
+
 ## 0.13.0
 
 ### Minor Changes
diff --git a/packages/deploy/package.json b/packages/deploy/package.json
index aa8f60188..6c6ef2123 100644
--- a/packages/deploy/package.json
+++ b/packages/deploy/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@openfn/deploy",
-  "version": "0.13.0",
+  "version": "0.13.1",
   "description": "Deploy projects to Lightning instances",
   "type": "module",
   "exports": {
diff --git a/packages/deploy/src/index.ts b/packages/deploy/src/index.ts
index 7aeae9e12..d5aaad97e 100644
--- a/packages/deploy/src/index.ts
+++ b/packages/deploy/src/index.ts
@@ -117,7 +117,7 @@ export async function deploy(config: DeployConfig, logger: Logger) {
     spec.errors.forEach((e: any) => logger.warn(`${e.path} :: ${e.message}`));
     throw new DeployError(`${config.specPath} has errors`, 'VALIDATION_ERROR');
   }
-  const nextState = mergeSpecIntoState(state, spec.doc, logger);
+  const nextState = mergeSpecIntoState(state, spec.doc);
 
   validateProjectState(nextState);
 
diff --git a/packages/deploy/src/stateTransform.ts b/packages/deploy/src/stateTransform.ts
index 69e28e20f..e40388474 100644
--- a/packages/deploy/src/stateTransform.ts
+++ b/packages/deploy/src/stateTransform.ts
@@ -21,7 +21,6 @@ import {
   assignIfTruthy,
 } from './utils';
 import { DeployError } from './deployError';
-import { Logger } from '@openfn/logger/dist';
 
 function stringifyJobBody(body: SpecJobBody): string {
   if (typeof body === 'object') {
@@ -300,8 +299,7 @@ function mergeEdges(
 // Prepare the next state, based on the current state and the spec.
 export function mergeSpecIntoState(
   oldState: ProjectState,
-  spec: ProjectSpec,
-  logger?: Logger
+  spec: ProjectSpec
 ): ProjectState {
   const nextCredentials = Object.fromEntries(
     splitZip(oldState.project_credentials || {}, spec.credentials || {}).map(
@@ -462,14 +460,7 @@ export function mergeSpecIntoState(
         }
 
         if (!specWorkflow && !isEmpty(stateWorkflow || {})) {
-          logger?.error('Critical error! Cannot continue');
-          logger?.error(
-            'Workflow found in project state but not spec:',
-            stateWorkflow?.name
-              ? `${stateWorkflow.name} (${stateWorkflow?.id})`
-              : stateWorkflow?.id
-          );
-          process.exit(1);
+          return [workflowKey, { id: stateWorkflow!.id, delete: true }];
         }
 
         return [
@@ -656,16 +647,16 @@ export function toProjectPayload(state: ProjectState): ProjectPayload {
   // the server expects lists of jobs, triggers, and edges, so we need to
   // convert the keyed objects into lists.
 
-  const workflows: ProjectPayload['workflows'] = Object.values(
-    state.workflows
-  ).map((workflow) => {
-    return {
-      ...workflow,
-      jobs: Object.values(workflow.jobs),
-      triggers: Object.values(workflow.triggers),
-      edges: Object.values(workflow.edges),
-    };
-  });
+  const workflows: ProjectPayload['workflows'] = Object.values(state.workflows)
+    .filter((workflow) => !workflow.delete)
+    .map((workflow) => {
+      return {
+        ...workflow,
+        jobs: Object.values(workflow.jobs),
+        triggers: Object.values(workflow.triggers),
+        edges: Object.values(workflow.edges),
+      };
+    });
 
   const project_credentials: ProjectPayload['project_credentials'] =
     Object.values(state.project_credentials);
diff --git a/packages/deploy/test/stateTransform.test.ts b/packages/deploy/test/stateTransform.test.ts
index 8b55dbcb9..7d8163581 100644
--- a/packages/deploy/test/stateTransform.test.ts
+++ b/packages/deploy/test/stateTransform.test.ts
@@ -401,6 +401,22 @@ test('toNextState removing a job and edge', (t) => {
   t.deepEqual(result, existingState);
 });
 
+test('toNextState deleting a whole workflow', (t) => {
+  let existingState = fullExampleState();
+  let spec = fullExampleSpec();
+
+  delete spec.workflows['workflow-one'];
+
+  let result = mergeSpecIntoState(existingState, spec);
+
+  jp.apply(existingState, '$.workflows["workflow-one"]', (value) => ({
+    id: value.id,
+    delete: true,
+  }));
+
+  t.deepEqual(result, existingState);
+});
+
 test('toNextState with for kafka trigger', (t) => {
   const state = { workflows: {} };
   const spec = {
@@ -1133,10 +1149,7 @@ test('toNextState resolves channel destination_credential to id', (t) => {
 
   const result = mergeSpecIntoState(state, spec);
 
-  t.is(
-    result.channels['webhook-out'].destination_credential_id,
-    'cred-id-123'
-  );
+  t.is(result.channels['webhook-out'].destination_credential_id, 'cred-id-123');
 });
 
 test('toNextState throws when channel references unknown credential', (t) => {