diff --git a/src/files_sub_source.cc b/src/files_sub_source.cc
index c9b670eef5b..363daf94ad4 100644
--- a/src/files_sub_source.cc
+++ b/src/files_sub_source.cc
@@ -97,6 +97,7 @@ files_sub_source::list_input_handle_key(listview_curses& lv, int ch)
                     auto& lss = lnav_data.ld_log_source;
                     auto lf = *fs.sb_iter;
 
+                    lf->set_indexing(true);
                     lss.find_data(lf) | [](auto ld) {
                         ld->set_visibility(true);
                         lnav_data.ld_log_source.text_filters_changed();
@@ -136,6 +137,7 @@ files_sub_source::list_input_handle_key(listview_curses& lv, int ch)
                           auto lf = *fs.sb_iter;
 
                           lss.find_data(lf) | [](auto ld) {
+                              ld->get_file_ptr()->set_indexing(!ld->ld_visible);
                               ld->set_visibility(!ld->ld_visible);
                           };
 
diff --git a/src/lnav.indexing.cc b/src/lnav.indexing.cc
index 75547413054..034e1941ffe 100644
--- a/src/lnav.indexing.cc
+++ b/src/lnav.indexing.cc
@@ -330,11 +330,12 @@ rebuild_indexes(nonstd::optional<ui_clock::time_point> deadline)
                 for_each(pair.second.begin(),
                          pair.second.end(),
                          [&dupe_name](auto& lf) {
-                             log_info("Hiding duplicate file: %s",
-                                      lf->get_filename().c_str());
-                             lf->mark_as_duplicate(dupe_name);
-                             lnav_data.ld_log_source.find_data(lf) |
-                                 [](auto ld) { ld->set_visibility(false); };
+                             if (lf->mark_as_duplicate(dupe_name)) {
+                                 log_info("Hiding duplicate file: %s",
+                                          lf->get_filename().c_str());
+                                 lnav_data.ld_log_source.find_data(lf) |
+                                     [](auto ld) { ld->set_visibility(false); };
+                             }
                          });
                 reload = true;
             }
@@ -373,9 +374,9 @@ rebuild_indexes(nonstd::optional<ui_clock::time_point> deadline)
             }
         }
 
+        auto* tss = tc->get_sub_source();
+        lnav_data.ld_filter_status_source.update_filtered(tss);
         if (retval.rir_changes > 0) {
-            auto* tss = tc->get_sub_source();
-            lnav_data.ld_filter_status_source.update_filtered(tss);
             lnav_data.ld_scroll_broadcaster(tc);
         }
     };
diff --git a/src/lnav_commands.cc b/src/lnav_commands.cc
index 7f14b6032af..5a9e09ef619 100644
--- a/src/lnav_commands.cc
+++ b/src/lnav_commands.cc
@@ -3321,8 +3321,10 @@ com_file_visibility(exec_context& ec,
             if (only_this_file) {
                 for (const auto& ld : lnav_data.ld_log_source) {
                     ld->set_visibility(false);
+                    ld->get_file_ptr()->set_indexing(false);
                 }
             }
+            lf->set_indexing(make_visible);
             lnav_data.ld_log_source.find_data(lf) |
                 [make_visible](auto ld) { ld->set_visibility(make_visible); };
             tc->get_sub_source()->text_filters_changed();
@@ -3375,6 +3377,7 @@ com_file_visibility(exec_context& ec,
 
             if (!ec.ec_dry_run) {
                 ld_opt | [make_visible](auto ld) {
+                    ld->get_file_ptr()->set_indexing(make_visible);
                     ld->set_visibility(make_visible);
                 };
             }
diff --git a/src/logfile.cc b/src/logfile.cc
index 9423ca309ac..3d3392e8e0a 100644
--- a/src/logfile.cc
+++ b/src/logfile.cc
@@ -1193,14 +1193,21 @@ logfile::find_from_time(const timeval& tv) const
     return retval;
 }
 
-void
+bool
 logfile::mark_as_duplicate(const std::string& name)
 {
+    safe::WriteAccess<safe_notes> notes(this->lf_notes);
+
+    auto iter = notes->find(note_type::duplicate);
+    if (iter != notes->end()) {
+        return false;
+    }
+
     this->lf_indexing = false;
     this->lf_options.loo_is_visible = false;
-    this->lf_notes.writeAccess()->emplace(
-        note_type::duplicate,
-        fmt::format(FMT_STRING("hiding duplicate of {}"), name));
+    notes->emplace(note_type::duplicate,
+                   fmt::format(FMT_STRING("hiding duplicate of {}"), name));
+    return true;
 }
 
 void
diff --git a/src/logfile.hh b/src/logfile.hh
index e21cb6252a4..98a5edc59a3 100644
--- a/src/logfile.hh
+++ b/src/logfile.hh
@@ -195,7 +195,7 @@ public:
         this->adjust_content_time(-1, tv);
     }
 
-    void mark_as_duplicate(const std::string& name);
+    bool mark_as_duplicate(const std::string& name);
 
     const logfile_open_options& get_open_options() const
     {
@@ -356,6 +356,8 @@ public:
 
     bool is_indexing() const { return this->lf_indexing; }
 
+    void set_indexing(bool val) { this->lf_indexing = val; }
+
     /** Check the invariants for this object. */
     bool invariant()
     {
diff --git a/src/session_data.cc b/src/session_data.cc
index 69fe2b32a12..27d16d576a4 100644
--- a/src/session_data.cc
+++ b/src/session_data.cc
@@ -926,16 +926,15 @@ load_session()
             log_debug("found state for file: %s %d",
                       lf->get_content_id().c_str(),
                       iter->second.fs_is_visible);
-            lnav_data.ld_log_source.find_data(lf) | [iter](auto ld) {
-                ld->set_visibility(iter->second.fs_is_visible);
-            };
-            if (!iter->second.fs_is_visible) {
-                if (lf->get_format() != nullptr) {
-                    log_changes = true;
-                } else {
-                    text_changes = true;
-                }
-            }
+            lnav_data.ld_log_source.find_data(lf) |
+                [iter, &log_changes](auto ld) {
+                    if (ld->ld_visible != iter->second.fs_is_visible) {
+                        ld->get_file_ptr()->set_indexing(
+                            iter->second.fs_is_visible);
+                        ld->set_visibility(iter->second.fs_is_visible);
+                        log_changes = true;
+                    }
+                };
         }
 
         if (log_changes) {
diff --git a/src/views_vtab.cc b/src/views_vtab.cc
index ba19fec3130..2522b67233a 100644
--- a/src/views_vtab.cc
+++ b/src/views_vtab.cc
@@ -1265,6 +1265,7 @@ CREATE TABLE lnav_view_files (
 
         auto& ld = *iter;
         if (ld->ld_visible != visible) {
+            ld->get_file_ptr()->set_indexing(visible);
             ld->set_visibility(visible);
             lss.text_filters_changed();
         }