diff --git a/openwisp-config/files/sbin/openwisp-update-config.lua b/openwisp-config/files/sbin/openwisp-update-config.lua
index 2df5e34..d5deaa4 100755
--- a/openwisp-config/files/sbin/openwisp-update-config.lua
+++ b/openwisp-config/files/sbin/openwisp-update-config.lua
@@ -32,7 +32,7 @@ local test_root_dir = working_dir .. '/update-test'
 local remote_dir = openwisp_dir .. '/remote'
 local remote_config_dir = remote_dir .. '/etc/config'
 local stored_dir = openwisp_dir .. '/stored'
-local stored_config_dir = openwisp_dir .. '/etc/config'
+local stored_config_dir = stored_dir .. '/etc/config'
 local added_file = openwisp_dir .. '/added.list'
 local modified_file = openwisp_dir .. '/modified.list'
 local get_standard = function() return uci.cursor(standard_config_dir) end
@@ -84,8 +84,8 @@ if lfs.attributes(remote_config_dir, 'mode') == 'directory' then
                     if section_stored == nil then
                         utils.remove_uci_options(standard, file, section)
                     -- section is in the backup configuration -> restore
-                    -- delete all options first
                     else
+                        -- delete all options first
                         for option, value in pairs(section) do
                             if not utils.starts_with_dot(option) then
                                 standard:delete(file, section['.name'], option)
@@ -148,7 +148,7 @@ if lfs.attributes(remote_config_dir, 'mode') == 'directory' then
         -- ensure we are acting on a file
         if lfs.attributes(remote_path, 'mode') == 'file' then
             -- if there's no backup of the file yet, create one
-            if not utils.file_exists(stored_path) then
+            if (not utils.file_exists(stored_path) and not utils.file_exists(remote_path)) then
                 os.execute('cp '..standard_path..' '..stored_path)
             end
             -- MERGE mode
diff --git a/openwisp-config/tests/test_update_config.lua b/openwisp-config/tests/test_update_config.lua
index 051a6bf..6265f8f 100644
--- a/openwisp-config/tests/test_update_config.lua
+++ b/openwisp-config/tests/test_update_config.lua
@@ -7,6 +7,7 @@ local update_config = assert(loadfile("../files/sbin/openwisp-update-config.lua"
 local write_dir = './update-test/'
 local config_dir = write_dir .. 'etc/config/'
 local openwisp_dir = './openwisp/'
+local stored_dir = openwisp_dir .. '/stored/'
 local remote_config_dir = openwisp_dir .. 'remote/etc/config'
 
 local function string_count(base, pattern)
@@ -38,8 +39,8 @@ TestUpdateConfig = {
         os.execute('echo restore-me > '..openwisp_dir..'/stored/etc/restore-me')
         os.execute('echo /etc/restore-me > '..openwisp_dir..'/modified.list')
         -- this file is stored in the backup
-        os.execute('mkdir -p ' .. openwisp_dir ..'etc/config/')
-        os.execute("cp ./update/stored_wireless " ..openwisp_dir.. '/etc/config/wireless')
+        os.execute('mkdir -p ' .. stored_dir ..'etc/config/')
+        os.execute("cp ./update/stored_wireless " ..stored_dir.. '/etc/config/wireless')
     end,
     tearDown = function()
         os.execute('rm -rf ' .. write_dir)
@@ -123,12 +124,12 @@ function TestUpdateConfig.test_update()
     luaunit.assertEquals(restoreFile:read('*all'), 'restore-me\n')
     luaunit.assertNil(io.open(openwisp_dir..'/stored/etc/restore-me'))
     -- ensure network configuration file is backed up
-    local storedNetworkFile = io.open(openwisp_dir .. '/etc/config/network')
+    local storedNetworkFile = io.open(stored_dir .. '/etc/config/network')
     luaunit.assertNotNil(storedNetworkFile)
     local initialNetworkFile = io.open('update/network')
     luaunit.assertEquals(storedNetworkFile:read('*all'), initialNetworkFile:read('*all'))
     -- ensure system configuration file is backed up
-    local storedSystemFile = io.open(openwisp_dir .. '/etc/config/system')
+    local storedSystemFile = io.open(stored_dir .. '/etc/config/system')
     luaunit.assertNotNil(storedSystemFile)
     local initialSystemFile = io.open('update/system')
     luaunit.assertEquals(storedSystemFile:read('*all'), initialSystemFile:read('*all'))