diff --git a/llvm/test/tools/UpdateTestChecks/update_test_checks/Inputs/conflict.ll b/llvm/test/tools/UpdateTestChecks/update_test_checks/Inputs/conflict.ll
new file mode 100644
--- /dev/null
+++ b/llvm/test/tools/UpdateTestChecks/update_test_checks/Inputs/conflict.ll
@@ -0,0 +1,8 @@
+; RUN: opt < %s -instcombine -S | FileCheck %s
+; RUN: opt < %s -vectorize-slp -S | FileCheck %s
+
+define i32 @example(i32 %X, i32 %Y) {
+  %Z = sub i32 %X, %Y
+  %Q = add i32 %Z, %Y
+  ret i32 %Q
+}
diff --git a/llvm/test/tools/UpdateTestChecks/update_test_checks/prefix_conflicts.test b/llvm/test/tools/UpdateTestChecks/update_test_checks/prefix_conflicts.test
new file mode 100644
--- /dev/null
+++ b/llvm/test/tools/UpdateTestChecks/update_test_checks/prefix_conflicts.test
@@ -0,0 +1,4 @@
+# Verify the script warns about conflicts of prefix in multiple run lines
+# RUN: cp -f %S/Inputs/conflict.ll %t.ll
+# RUN: %update_test_checks %t.ll 2>&1 | FileCheck %s
+# CHECK: Prefix CHECK had conflicting output from different RUN lines for functions: example
diff --git a/llvm/utils/UpdateTestChecks/common.py b/llvm/utils/UpdateTestChecks/common.py
--- a/llvm/utils/UpdateTestChecks/common.py
+++ b/llvm/utils/UpdateTestChecks/common.py
@@ -272,8 +272,9 @@
         self._func_order.update({prefix: []})
 
   def finish_and_get_func_dict(self):
-    for prefix in self._get_failed_prefixes():
-      warn('Prefix %s had conflicting output from different RUN lines for all functions' % (prefix,))
+    for prefix, funcs in self._get_failed_prefixes():
+      warn('Prefix %s had conflicting output from different RUN lines for functions: %s' % (
+          prefix, ', '.join(funcs)))
     return self._func_dict
 
   def func_order(self):
@@ -336,15 +337,15 @@
         self._func_order[prefix].append(func)
 
   def _get_failed_prefixes(self):
-    # This returns the list of those prefixes that failed to match any function,
+    # This returns the list of those prefixes that failed to match some functions,
     # because there were conflicting bodies produced by different RUN lines, in
-    # all instances of the prefix. Effectively, this prefix is unused and should
-    # be removed.
+    # all instances of the prefix. This prefix needs to be split or removed.
     for prefix in self._func_dict:
-      if (self._func_dict[prefix] and 
-          (not [fct for fct in self._func_dict[prefix]
-                if self._func_dict[prefix][fct] is not None])):
-        yield prefix
+      if self._func_dict[prefix]:
+        funcs = [fct for fct in self._func_dict[prefix]
+                 if self._func_dict[prefix][fct] is None]
+        if funcs:
+            yield (prefix, funcs)
 
 
 ##### Generator of LLVM IR CHECK lines