diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -1690,6 +1690,27 @@
             if not complete:
                 numupdates += 1
                 tocomplete.append((f, args, msg))
+            else:
+                action = mresult.getfile(f)[0]
+                if action in (
+                    mergestatemod.ACTION_DELETED_CHANGED,
+                    mergestatemod.ACTION_CHANGED_DELETED,
+                ):
+                    # the merge was conflicting and either the mergetool
+                    # choosed by the user or the user themselves on the prompt
+                    # made a choice.
+                    # If the changed file was kept, at commit we end up using
+                    # the same filelog. This is not completely correct behavior
+                    # as the new file post merge also represents that a
+                    # conflicting change-delete merge was resolved in it's
+                    # favor. Hence we will like to create a new filenode for
+                    # that. Let's store this in mergestate extras
+                    repo.ui.debug(
+                        b"file %s had %s conflicts and mergetool resolved it, storing info in commitinfo\n"
+                        % (f, action)
+                    )
+
+                    ms.addcommitinfo(f, {b'FORCE_NEW_FILENODE': b'yes'})
 
         # merge
         for f, args, msg in tocomplete:
diff --git a/tests/test-merge-criss-cross.t b/tests/test-merge-criss-cross.t
--- a/tests/test-merge-criss-cross.t
+++ b/tests/test-merge-criss-cross.t
@@ -537,6 +537,16 @@
   $ hg merge 'desc("updating-both-file")' -t :local
   1 files updated, 1 files merged, 0 files removed, 0 files unresolved
   (branch merge, don't forget to commit)
+  $ hg debugmergestate
+  local (working copy): 7801bc9b9899de5e304bd162cafde9b78e10ab9b
+  other (merge rev): 9b610631ab29024c5f44af7d2c19658ef8f8f071
+  file: the-file (state "r")
+    local path: the-file (hash 0000000000000000000000000000000000000000, flags "")
+    ancestor path: the-file (node 4b69178b9bdae28b651393b46e631427a72f217a)
+    other path: the-file (node 59e363a07dc876278f0e41756236f30213b6b460)
+    extra: FORCE_NEW_FILENODE = yes
+    extra: ancestorlinknode = 955800955977bd6c103836ee3e437276e940a589
+  extra: other-file (filenode-source = other)
   $ hg ci -m "merge-deleting-the-file-from-deleted"
   $ hg manifest
   other-file
@@ -550,6 +560,15 @@
   $ hg merge 'desc("delete-the-file")' -t :other
   0 files updated, 0 files merged, 1 files removed, 0 files unresolved
   (branch merge, don't forget to commit)
+  $ hg debugmergestate
+  local (working copy): 9b610631ab29024c5f44af7d2c19658ef8f8f071
+  other (merge rev): 7801bc9b9899de5e304bd162cafde9b78e10ab9b
+  file: the-file (state "r")
+    local path: the-file (hash 6d2e02da5a9fe0691363dc6b573845fa271eaa35, flags "")
+    ancestor path: the-file (node 4b69178b9bdae28b651393b46e631427a72f217a)
+    other path: the-file (node 0000000000000000000000000000000000000000)
+    extra: FORCE_NEW_FILENODE = yes
+    extra: ancestorlinknode = 955800955977bd6c103836ee3e437276e940a589
   $ hg ci -m "merge-deleting-the-file-from-updated"
   created new head
   $ hg manifest
@@ -564,6 +583,16 @@
   $ hg merge 'desc("updating-both-file")' -t :other
   1 files updated, 1 files merged, 0 files removed, 0 files unresolved
   (branch merge, don't forget to commit)
+  $ hg debugmergestate
+  local (working copy): 7801bc9b9899de5e304bd162cafde9b78e10ab9b
+  other (merge rev): 9b610631ab29024c5f44af7d2c19658ef8f8f071
+  file: the-file (state "r")
+    local path: the-file (hash 0000000000000000000000000000000000000000, flags "")
+    ancestor path: the-file (node 4b69178b9bdae28b651393b46e631427a72f217a)
+    other path: the-file (node 59e363a07dc876278f0e41756236f30213b6b460)
+    extra: FORCE_NEW_FILENODE = yes
+    extra: ancestorlinknode = 955800955977bd6c103836ee3e437276e940a589
+  extra: other-file (filenode-source = other)
   $ hg ci -m "merge-keeping-the-file-from-deleted"
   created new head
   $ hg manifest
@@ -581,6 +610,15 @@
   $ hg merge 'desc("delete-the-file")' -t :local
   0 files updated, 1 files merged, 0 files removed, 0 files unresolved
   (branch merge, don't forget to commit)
+  $ hg debugmergestate
+  local (working copy): 9b610631ab29024c5f44af7d2c19658ef8f8f071
+  other (merge rev): 7801bc9b9899de5e304bd162cafde9b78e10ab9b
+  file: the-file (state "r")
+    local path: the-file (hash 6d2e02da5a9fe0691363dc6b573845fa271eaa35, flags "")
+    ancestor path: the-file (node 4b69178b9bdae28b651393b46e631427a72f217a)
+    other path: the-file (node 0000000000000000000000000000000000000000)
+    extra: FORCE_NEW_FILENODE = yes
+    extra: ancestorlinknode = 955800955977bd6c103836ee3e437276e940a589
   $ hg ci -m "merge-keeping-the-file-from-updated"
   created new head
   $ hg manifest