diff --git a/include/revng/PipelineC/Prototypes.h b/include/revng/PipelineC/Prototypes.h
index 4230c2c5b..f2c3d4eb2 100644
--- a/include/revng/PipelineC/Prototypes.h
+++ b/include/revng/PipelineC/Prototypes.h
@@ -364,7 +364,8 @@ bool rp_manager_container_deserialize(rp_manager *manager,
                                       rp_step *step,
                                       const char *container_name,
                                       const char *content,
-                                      uint64_t size);
+                                      uint64_t size,
+                                      rp_invalidations *invalidations);
 LENGTH_HINT(rp_manager_container_deserialize, 3, 4)
 
 /**
diff --git a/include/revng/Pipes/PipelineManager.h b/include/revng/Pipes/PipelineManager.h
index 80023eb1c..573fea5c3 100644
--- a/include/revng/Pipes/PipelineManager.h
+++ b/include/revng/Pipes/PipelineManager.h
@@ -105,9 +105,10 @@ public:
   const pipeline::Step::AnalysisValueType &
   getAnalysis(const pipeline::AnalysisReference &Reference) const;
 
-  llvm::Error deserializeContainer(pipeline::Step &Step,
-                                   llvm::StringRef ContainerName,
-                                   const llvm::MemoryBuffer &Buffer);
+  llvm::Expected<pipeline::InvalidationMap>
+  deserializeContainer(pipeline::Step &Step,
+                       llvm::StringRef ContainerName,
+                       const llvm::MemoryBuffer &Buffer);
 
   const pipeline::Context &context() const { return *PipelineContext; }
 
diff --git a/lib/PipelineC/PipelineC.cpp b/lib/PipelineC/PipelineC.cpp
index a2011aef3..65eca4ae0 100644
--- a/lib/PipelineC/PipelineC.cpp
+++ b/lib/PipelineC/PipelineC.cpp
@@ -387,20 +387,25 @@ static bool _rp_manager_container_deserialize(rp_manager *manager,
                                               rp_step *step,
                                               const char *container_name,
                                               const char *content,
-                                              uint64_t size) {
+                                              uint64_t size,
+                                              rp_invalidations *invalidations) {
   revng_check(manager != nullptr);
   revng_check(step != nullptr);
   revng_check(container_name != nullptr);
   revng_check(content != nullptr);
 
-  auto Buffer = llvm::MemoryBuffer::getMemBuffer(llvm::StringRef(content, size),
-                                                 "",
-                                                 false);
-  auto Error = manager->deserializeContainer(*step, container_name, *Buffer);
-  if (!!Error) {
-    llvm::consumeError(std::move(Error));
+  llvm::StringRef String(content, size);
+  auto Buffer = llvm::MemoryBuffer::getMemBuffer(String, "", false);
+  auto MaybeInvalidations = manager->deserializeContainer(*step,
+                                                          container_name,
+                                                          *Buffer);
+  if (not MaybeInvalidations) {
+    llvm::consumeError(MaybeInvalidations.takeError());
     return false;
   }
+
+  ExistingOrNew<rp_invalidations> Invalidations(invalidations);
+  *Invalidations = MaybeInvalidations.get();
   return true;
 }
 
diff --git a/lib/Pipes/PipelineManager.cpp b/lib/Pipes/PipelineManager.cpp
index ca230a2c1..c57e57c90 100644
--- a/lib/Pipes/PipelineManager.cpp
+++ b/lib/Pipes/PipelineManager.cpp
@@ -272,7 +272,7 @@ llvm::Error PipelineManager::storeStepToDisk(llvm::StringRef StepName) {
   return StorageClient->commit();
 }
 
-llvm::Error
+llvm::Expected<InvalidationMap>
 PipelineManager::deserializeContainer(pipeline::Step &Step,
                                       llvm::StringRef ContainerName,
                                       const llvm::MemoryBuffer &Buffer) {
@@ -286,12 +286,14 @@ PipelineManager::deserializeContainer(pipeline::Step &Step,
   if (auto Error = Container.deserialize(Buffer); !!Error)
     return Error;
 
-  recalculateAllPossibleTargets();
+  auto MaybeInvalidations = invalidateAllPossibleTargets();
+  if (not MaybeInvalidations)
+    return MaybeInvalidations.takeError();
 
   if (auto Error = storeStepToDisk(Step.getName()); !!Error)
     return Error;
 
-  return Error::success();
+  return MaybeInvalidations.get();
 }
 
 llvm::Error PipelineManager::store(const PipelineFileMapping &Mapping) {
diff --git a/python/revng/api/manager.py b/python/revng/api/manager.py
index 047215779..e50db38af 100644
--- a/python/revng/api/manager.py
+++ b/python/revng/api/manager.py
@@ -339,12 +339,18 @@ class Manager:
         _out = _api.rp_manager_create_global_copy(self._manager, _name)
         return make_python_string(_out)
 
-    def set_input(self, container_name: str, content: bytes, _key=None):
+    def set_input(self, container_name: str, content: bytes, _key=None) -> Invalidations:
         step_ptr = self._get_step_ptr("begin")
 
         _content = ffi.from_buffer(content)
+        invalidations = Invalidations()
         success = _api.rp_manager_container_deserialize(
-            self._manager, step_ptr, make_c_string(container_name), _content, len(_content)
+            self._manager,
+            step_ptr,
+            make_c_string(container_name),
+            _content,
+            len(_content),
+            invalidations._invalidations,
         )
 
         if not success:
@@ -352,6 +358,8 @@ class Manager:
                 f"Failed loading user provided input for container {container_name}"
             )
 
+        return invalidations
+
     def get_pipeline_description(self):
         return self._description_str