diff --git a/.changeset/fluffy-eggs-wink.md b/.changeset/fluffy-eggs-wink.md
new file mode 100644
index 000000000..7395a2356
--- /dev/null
+++ b/.changeset/fluffy-eggs-wink.md
@@ -0,0 +1,5 @@
+---
+'@openfn/project': patch
+---
+
+On merge, warn when projects may have diverged
diff --git a/.changeset/weak-gifts-work.md b/.changeset/weak-gifts-work.md
new file mode 100644
index 000000000..ea45311f8
--- /dev/null
+++ b/.changeset/weak-gifts-work.md
@@ -0,0 +1,5 @@
+---
+'@openfn/cli': patch
+---
+
+Warn when merging projects which may have diverged
diff --git a/packages/cli/src/merge/command.ts b/packages/cli/src/merge/command.ts
index f61db6750..a07447e1d 100644
--- a/packages/cli/src/merge/command.ts
+++ b/packages/cli/src/merge/command.ts
@@ -1,6 +1,6 @@
 import yargs from 'yargs';
 import { Opts } from '../options';
-import { ensure, build } from '../util/command-builders';
+import { ensure, build, override } from '../util/command-builders';
 import * as o from '../options';
 
 export type MergeOptions = Required<
@@ -12,6 +12,7 @@ export type MergeOptions = Required<
     | 'removeUnmapped'
     | 'workflowMappings'
     | 'log'
+    | 'force'
   >
 >;
 
@@ -21,6 +22,9 @@ const options = [
   o.removeUnmapped,
   o.workflowMappings,
   o.log,
+  override(o.force, {
+    description: 'Force a merge even when workflows are incompatible',
+  }),
 ];
 
 const mergeCommand: yargs.CommandModule = {
diff --git a/packages/cli/src/merge/handler.ts b/packages/cli/src/merge/handler.ts
index 4c767df83..fe3ed2283 100644
--- a/packages/cli/src/merge/handler.ts
+++ b/packages/cli/src/merge/handler.ts
@@ -55,6 +55,7 @@ const mergeHandler = async (options: MergeOptions, logger: Logger) => {
   const final = Project.merge(sourceProject, targetProject, {
     removeUnmapped: options.removeUnmapped,
     workflowMappings: options.workflowMappings,
+    force: options.force,
   });
   const yaml = final.serialize('state', { format: 'yaml' });
   await fs.writeFile(finalPath, yaml);
diff --git a/packages/project/src/merge/merge-project.ts b/packages/project/src/merge/merge-project.ts
index 09becaae5..9d3b7b1a6 100644
--- a/packages/project/src/merge/merge-project.ts
+++ b/packages/project/src/merge/merge-project.ts
@@ -1,4 +1,3 @@
-import { Workflow } from '@openfn/lexicon';
 import { defaultsDeep, isEmpty } from 'lodash-es';
 
 import { Project } from '../Project';
@@ -6,12 +5,12 @@ import { mergeWorkflows } from './merge-node';
 import mapUuids from './map-uuids';
 import baseMerge from '../util/base-merge';
 import getDuplicates from '../util/get-duplicates';
+import Workflow from '../Workflow';
 
 export type MergeProjectOptions = Partial<{
   workflowMappings: Record<string, string>; // <source, target>
   removeUnmapped: boolean;
-
-  force: boolean; // TODO not implemented yet
+  force: boolean;
 }>;
 
 /**
@@ -56,6 +55,27 @@ export function merge(
     return !!options?.workflowMappings[w.id];
   });
 
+  // mergeability
+  const potentialConflicts: Record<string, string> = {};
+  for (const sourceWorkflow of sourceWorkflows) {
+    const targetId =
+      options.workflowMappings?.[sourceWorkflow.id] ?? sourceWorkflow.id;
+    const targetWorkflow = target.getWorkflow(targetId);
+    if (targetWorkflow && !sourceWorkflow.canMergeInto(targetWorkflow)) {
+      potentialConflicts[sourceWorkflow.name] = targetWorkflow?.name;
+    }
+  }
+
+  if (Object.keys(potentialConflicts).length && !options?.force) {
+    throw new Error(
+      `The below workflows can't be merged directly without losing data\n${Object.entries(
+        potentialConflicts
+      )
+        .map(([from, to]) => `${from} → ${to}`)
+        .join('\n')}\nPass --force to force the merge anyway`
+    );
+  }
+
   for (const sourceWorkflow of sourceWorkflows) {
     const targetId =
       options.workflowMappings?.[sourceWorkflow.id] ?? sourceWorkflow.id;
diff --git a/packages/project/test/project.test.ts b/packages/project/test/project.test.ts
index ac5475322..8a0ac6bf1 100644
--- a/packages/project/test/project.test.ts
+++ b/packages/project/test/project.test.ts
@@ -2,7 +2,7 @@
 import test from 'ava';
 import type { Provisioner } from '@openfn/lexicon/lightning';
 import { Project } from '../src/Project';
-import generateWorkflow from '../src/gen/generator';
+import generateWorkflow, { generateProject } from '../src/gen/generator';
 
 // TODO move to fixtures and re-use?
 // Or use util function instead?
@@ -154,3 +154,34 @@ test('should return UUIDs for everything', (t) => {
     },
   });
 });
+
+test('incompatible-merge: should throw error when merge is incompatible', (t) => {
+  const source = generateWorkflow('trigger-x');
+  source.pushHistory(source.getVersionHash());
+  const target = generateWorkflow('trigger-y');
+  target.pushHistory(target.getVersionHash());
+
+  t.false(source.canMergeInto(target));
+
+  const sourceProject = new Project({ workflows: [source] });
+  const targetProject = new Project({ workflows: [target] });
+  t.throws(() => Project.merge(sourceProject, targetProject), {
+    message: `The below workflows can't be merged directly without losing data\nWorkflow → Workflow\nPass --force to force the merge anyway`,
+  });
+});
+
+test('incompatible-merge-force: should ignore incompatiblity and merge when forced', (t) => {
+  // same as the above test with force
+  const source = generateWorkflow('trigger-x');
+  source.pushHistory(source.getVersionHash());
+  const target = generateWorkflow('trigger-y');
+  target.pushHistory(target.getVersionHash());
+
+  t.false(source.canMergeInto(target));
+
+  const sourceProject = new Project({ workflows: [source] });
+  const targetProject = new Project({ workflows: [target] });
+  t.notThrows(() =>
+    Project.merge(sourceProject, targetProject, { force: true })
+  );
+});