diff --git a/psptool/__main__.py b/psptool/__main__.py
index 03e61a6..827f161 100755
--- a/psptool/__main__.py
+++ b/psptool/__main__.py
@@ -123,7 +123,8 @@ def main():
         '-r idx:  specifies rom_index (default: 0)',
         '-d idx:  specifies directory_index',
         '-e idx:  specifies file_index',
-        '-s file: specifies subfile (i.e. the new file contents)',
+        '-s file: specifies substitution file (i.e. the new file contents)',
+        '(optional to allow plain re-signs)',
         '-o file: specifies outfile',
         '-p file: specifies file-stub (e.g. \'keys/id\') for the re-signing keys',
         '-a pass: specifies password for the re-signing keys'
@@ -239,7 +240,7 @@ def main():
         if args.directory_index is not None and args.file_index is not None and args.outfile is not None:
             file = psp.blob.roms[args.rom_index].directories[args.directory_index].files[args.file_index]
 
-            # Substituting an file is actually optional to allow plain re-signs
+            # Substituting a file is actually optional to allow plain re-signs
             if args.subfile is not None:
                 with open(args.subfile, 'rb') as f:
                     sub_binary = f.read()
diff --git a/psptool/directory.py b/psptool/directory.py
index ed05023..609fe7f 100644
--- a/psptool/directory.py
+++ b/psptool/directory.py
@@ -212,7 +212,10 @@ def update_entry_fields(self, file: File, type_, size, offset):
             if my_entry.type == file.type:
                 entry = my_entry
                 break
-        assert(entry is not None)
+        assert (entry is not None)
+
+        if entry.address_mode == 2 or entry.address_mode == 3:
+            offset -= self.buffer_offset
 
         # 2. Update fields
         entry.type = type_
diff --git a/psptool/file.py b/psptool/file.py
index b366f74..1baf87c 100644
--- a/psptool/file.py
+++ b/psptool/file.py
@@ -389,7 +389,7 @@ def move_buffer(self, new_address, size):
         current_address = self.get_address()
         move_offset = new_address - current_address
         self.buffer_offset += move_offset
-        self.buffer_size = int(ceil(size / self.ENTRY_ALIGNMENT)) * self.ENTRY_ALIGNMENT
+        self.buffer_size = size
 
         # update all directories' headers that point to this entry
         for directory in self.references: