diff --git a/src/slic3r/GUI/ConfigWizard.cpp b/src/slic3r/GUI/ConfigWizard.cpp
index 7dec1da12a..2a2becf445 100644
--- a/src/slic3r/GUI/ConfigWizard.cpp
+++ b/src/slic3r/GUI/ConfigWizard.cpp
@@ -3333,17 +3333,6 @@ bool ConfigWizard::priv::apply_config(AppConfig *app_config, PresetBundle *prese
     const auto enabled_vendors = appconfig_new.vendors();
     const auto enabled_vendors_old = app_config->vendors();
 
-    std::vector<std::string> used_repo_ids;
-    for (const auto& vendor : enabled_vendors) {
-        const auto& it = bundles.find(vendor.first);
-        assert(it != bundles.end());
-        const std::string repo_id = it->second.vendor_profile->repo_id;
-        if (std::find(used_repo_ids.begin(), used_repo_ids.end(), repo_id) == used_repo_ids.end()) {
-            used_repo_ids.emplace_back(repo_id);
-        }
-    }
-    wxGetApp().plater()->get_preset_archive_database()->set_installed_printer_repositories(std::move(used_repo_ids));
-
     bool suppress_sla_printer = model_has_multi_part_objects(wxGetApp().model());
     PrinterTechnology preferred_pt = ptAny;
     auto get_preferred_printer_technology = [enabled_vendors, enabled_vendors_old, suppress_sla_printer](const std::string& bundle_name, const Bundle& bundle) {
@@ -3577,6 +3566,36 @@ bool ConfigWizard::priv::apply_config(AppConfig *app_config, PresetBundle *prese
         }
     }
 
+    // Save used repo into manifest.
+    std::vector<std::string> used_repo_ids;
+    for (const auto& vendor : enabled_vendors) {
+        // here vendor might be empty - it causes false has_installed_printers : 1 entries in manifest.
+        if (vendor.second.empty()){
+            continue;
+        }
+        bool not_empty = false;
+        for (const auto& it : vendor.second) {
+            if (!it.second.empty())  {
+                not_empty = true;
+                break;
+            }
+        }
+        if (!not_empty) {
+            continue;
+        }
+
+        const auto& it = bundles.find(vendor.first);
+        // This is a last resort solution of missing secret repo in manifest while some of its printers are installed.
+        if (it == bundles.end()) { 
+            continue;
+        }
+        const std::string repo_id = it->second.vendor_profile->repo_id;
+        if (std::find(used_repo_ids.begin(), used_repo_ids.end(), repo_id) == used_repo_ids.end()) {
+            used_repo_ids.emplace_back(repo_id);
+        }
+    }
+    wxGetApp().plater()->get_preset_archive_database()->set_installed_printer_repositories(std::move(used_repo_ids));
+
     // apply materials in app_config
     for (const std::string& section_name : {AppConfig::SECTION_FILAMENTS, AppConfig::SECTION_MATERIALS})
         if (appconfig_new.has_section(section_name))
diff --git a/src/slic3r/GUI/PresetArchiveDatabase.cpp b/src/slic3r/GUI/PresetArchiveDatabase.cpp
index ae77171d1a..f011b91d53 100644
--- a/src/slic3r/GUI/PresetArchiveDatabase.cpp
+++ b/src/slic3r/GUI/PresetArchiveDatabase.cpp
@@ -409,21 +409,44 @@ void PresetArchiveDatabase::set_installed_printer_repositories(const std::vector
 	// set correct repos as having installed printer
     for (const std::string &used_id : used_ids) {
 		// find archive with id and is used
+        std::vector<std::string> selected_uuid;
+        std::vector<std::string> unselected_uuid;
         for (const auto &archive : m_archive_repositories) {
             if (archive->get_manifest().id != used_id) {
 				continue;
 			}	
 			const std::string uuid = archive->get_uuid();
-
-            const auto& it = m_selected_repositories_uuid.find(uuid);
-            assert(it != m_selected_repositories_uuid.end());
-            if (it->second == false) {
-				continue;
-			}
-
-			// set archive as has installed printer
-            m_has_installed_printer_repositories_uuid[uuid] = true;
+            if (m_selected_repositories_uuid[uuid]) {
+                selected_uuid.emplace_back(uuid);
+            } else {
+                unselected_uuid.emplace_back(uuid);
+            }
 		}
+        
+        if (selected_uuid.empty() && unselected_uuid.empty()) {
+            // there is id in used_ids that is not in m_archive_repositories - BAD
+            assert(true);
+            continue;
+        } else if (selected_uuid.size() == 1){
+            // regular case
+             m_has_installed_printer_repositories_uuid[selected_uuid.front()] = true;
+        } else if (selected_uuid.size() > 1) {
+            // this should not happen, only one repo of same id should be selected (online / local conflict)
+            assert(true);
+            // select first one to solve the conflict
+            m_has_installed_printer_repositories_uuid[selected_uuid.front()] = true;
+            // unselect the rest
+            for (size_t i = 1; i < selected_uuid.size(); i++) {
+                m_selected_repositories_uuid[selected_uuid[i]] = false;
+            }
+        } else if (selected_uuid.empty()) {
+            // This is a rare case, where there are no selected repos with matching id but id has installed printers
+            // Repro: install printer, unselect repo in the next run of wizard, next, cancel wizard, run wizard again and press finish.
+            // Solution: Select the first unselected 
+            m_has_installed_printer_repositories_uuid[unselected_uuid.front()] = true;
+            m_selected_repositories_uuid[unselected_uuid.front()] = true;
+        }
+
 	}
     save_app_manifest_json();
 }
@@ -689,7 +712,7 @@ void PresetArchiveDatabase::clear_online_repos()
 {
 	auto it = m_archive_repositories.begin();
 	while (it != m_archive_repositories.end()) {
-		// Do not clean repos with local path (local repo) and with visibility filled (secret repo)
+		// Do not clean repos with local path (local repo).
         if ((*it)->get_manifest().tmp_path.empty()) {
 			it = m_archive_repositories.erase(it);
 		} else {