Index: ELF/LinkerScript.cpp
===================================================================
--- ELF/LinkerScript.cpp
+++ ELF/LinkerScript.cpp
@@ -813,7 +813,7 @@
   for (BaseCommand *Base : Sec.SectionCommands)
     if (!isa<InputSectionDescription>(*Base))
       return false;
-  return getInputSections(&Sec).empty();
+  return true;
 }
 
 void LinkerScript::adjustSectionsBeforeSorting() {
@@ -839,23 +839,23 @@
   // the previous sections. Only a few flags are needed to keep the impact low.
   uint64_t Flags = SHF_ALLOC;
 
-  for (BaseCommand *&Cmd : SectionCommands) {
+  for (BaseCommand *Cmd : SectionCommands) {
     auto *Sec = dyn_cast<OutputSection>(Cmd);
     if (!Sec)
       continue;
 
     // A live output section means that some input section was added to it. It
-    // might have been removed (gc, or empty synthetic section), but we at least
+    // might have been removed (if it was empty synthetic section), but we at least
     // know the flags.
     if (Sec->Live)
       Flags = Sec->Flags & (SHF_ALLOC | SHF_WRITE | SHF_EXECINSTR);
-    else
+
+    // We do not want to keep any special flags for output section in case it is empty.
+    bool IsEmpty = getInputSections(Sec).empty();
+    if (!Sec->Live || IsEmpty)
       Sec->Flags = Flags;
 
-    if (isDiscardable(*Sec)) {
-      Sec->Live = false;
-      Cmd = nullptr;
-    }
+    Sec->Live = !IsEmpty || !isDiscardable(*Sec);
   }
 
   // It is common practice to use very generic linker scripts. So for any
@@ -864,7 +864,9 @@
   // clutter the output.
   // We instead remove trivially empty sections. The bfd linker seems even
   // more aggressive at removing them.
-  llvm::erase_if(SectionCommands, [&](BaseCommand *Base) { return !Base; });
+  llvm::erase_if(SectionCommands, [&](BaseCommand *Base) {
+    return isa<OutputSection>(Base) && !cast<OutputSection>(Base)->Live;
+  });
 }
 
 void LinkerScript::adjustSectionsAfterSorting() {
Index: test/ELF/linkerscript/empty-link-order.test
===================================================================
--- test/ELF/linkerscript/empty-link-order.test
+++ test/ELF/linkerscript/empty-link-order.test
@@ -0,0 +1,10 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=arm-arm-none-eabi -o %t.o < /dev/null
+
+SECTIONS {
+  .foo : {
+    bar = .;
+    *(.ARM.exidx*)
+  }
+}
+# RUN: ld.lld %t.o -o %t --script %s