Index: llvm/trunk/lib/Linker/IRMover.cpp
===================================================================
--- llvm/trunk/lib/Linker/IRMover.cpp
+++ llvm/trunk/lib/Linker/IRMover.cpp
@@ -758,8 +758,18 @@
   }
 
   for (GlobalValue &SGV : *SrcM)
-    if (GlobalValue *DGV = getLinkedToGlobal(&SGV))
+    if (GlobalValue *DGV = getLinkedToGlobal(&SGV)) {
+      if (DGV->getType() == SGV.getType()) {
+        // If the types of DGV and SGV are the same, it means that DGV is from
+        // the source module and got added to DstM from a shared metadata.  We
+        // shouldn't map this type to itself in case the type's components get
+        // remapped to a new type from DstM (for instance, during the loop over
+        // SrcM->getIdentifiedStructTypes() below).
+        continue;
+      }
+
       TypeMap.addTypeMapping(DGV->getType(), SGV.getType());
+    }
 
   for (GlobalValue &SGV : SrcM->aliases())
     if (GlobalValue *DGV = getLinkedToGlobal(&SGV))
Index: llvm/trunk/test/LTO/X86/Inputs/type-mapping-bug3.ll
===================================================================
--- llvm/trunk/test/LTO/X86/Inputs/type-mapping-bug3.ll
+++ llvm/trunk/test/LTO/X86/Inputs/type-mapping-bug3.ll
@@ -0,0 +1,26 @@
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+; T2 is the non-opaque struct required to trigger the uniqued T2.0 and T3.0 to
+; respectively T2 and T3 in the destination module.
+%"T2" = type { %"T3"* }
+%"T3" = type opaque
+
+; Use/refer to T2 so it gets added as an IdentifiedStructType.  The debug
+; reference to !6 is required to transitively load the metadata !5.
+define void @a(%"T2") !dbg !6 {
+  ret void
+}
+
+!llvm.module.flags = !{!0, !1}
+!llvm.dbg.cu = !{!2}
+!0 = !{i32 1, !"ThinLTO", i32 0}
+!1 = !{i32 2, !"Debug Info Version", i32 3}
+!2 = distinct !DICompileUnit(language: DW_LANG_C_plus_plus, file: !3, retainedTypes: !4)
+!3 = !DIFile(filename: "f2", directory: "")
+!4 = !{!5}
+
+; This DICompositeType refers to !5 in type-mapping-bug3.ll
+!5 = !DICompositeType(tag: DW_TAG_structure_type, flags: DIFlagFwdDecl, identifier: "SHARED")
+
+!6 = distinct !DISubprogram(unit: !2)
Index: llvm/trunk/test/LTO/X86/type-mapping-bug3.ll
===================================================================
--- llvm/trunk/test/LTO/X86/type-mapping-bug3.ll
+++ llvm/trunk/test/LTO/X86/type-mapping-bug3.ll
@@ -0,0 +1,47 @@
+; RUN: opt -module-summary -o %t0.o %S/Inputs/type-mapping-bug3.ll
+; RUN: opt -module-summary -o %t1.o %s
+; RUN: llvm-lto2 run -o %t2 %t0.o %t1.o -r %t0.o,a,px -r %t1.o,b,px -r %t1.o,c,px -r %t1.o,d,
+;
+; Test for the issue described in https://bugs.llvm.org/show_bug.cgi?id=40312
+
+target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128"
+target triple = "x86_64-unknown-linux-gnu"
+
+; T2 is the non-opaque struct required to trigger the uniqued T2.0 and T3.0 to
+; respectively T2 and T3 in the destination module.
+%"T2" = type { %"T3"* }
+%"T3" = type opaque
+
+; Use/refer to T2 so it gets added as an IdentifiedStructType.
+define void @c(%"T2") {
+    unreachable
+}
+
+; The global declaration that causes the assertion when its type is mapped to
+; itself incorrectly.
+declare void @d(%"T3"*)
+
+define void @b() {
+entry:
+  %f.addr = alloca %"T3"*load %"T3"*, %"T3"** %f.addr
+
+  ; The call with the getCalledValue() vs getCalledFunction() mismatch.
+  call void @d(%"T3"* %0)
+  unreachable
+}
+
+!llvm.dbg.cu = !{!2}
+!llvm.module.flags = !{!0, !1}
+!0 = !{i32 1, !"ThinLTO", i32 0}
+!1 = !{i32 2, !"Debug Info Version", i32 3}
+!2 = distinct !DICompileUnit(language: DW_LANG_C_plus_plus, file: !3, retainedTypes: !4)
+!3 = !DIFile(filename: "f1", directory: "")
+!4 = !{!5}
+
+; This DICompositeType is referenced by !5 in Inputs/type-mapping-bug3.ll
+; causing the function type in !7 to be added to its module.
+!5 = !DICompositeType(tag: DW_TAG_structure_type, templateParams: !6, identifier: "SHARED")
+!6 = !{!7}
+
+; The reference to d and T3 that gets loaded into %t0.o
+!7 = !DITemplateValueParameter(value: void (%"T3"*)* @d)