Thanks that you found a time for my problem.

I will tell you how to reproduce missnumbering.

1) Make an empty Word document based on the default template.
2) Type this text to it (without minuses):
--------------------------
This is subdocument.
First list:
One
Two
Three
Second list:
One
Two
Three
-------------------------

3) Create a new style named 'MyNumberedList' with single-leveled numbering.
I used predefined numbering template 1. 2. 3. ... for this style (to make
such a style press 'Format'-'Styles and Formatting'-'Create style' in the
sidebar. Then press 'Format' button in new window and 'Numbering' in menu.
Select numbering template and press OK. Enter style name and press OK)
4) Mark all 'One', 'Two' and 'Three' lines with this style and select
'Restart numbering' in right-mouse-button-menu for both 'One' lines in the
document. You will get something like this:
--------------------------
This is subdocument.
First list:
1. One
2. Two
3. Three
Second list:
1. One
2. Two
3. Three
-------------------------

5) Save this file as 'SubDocument.doc'.
6) Close file.
7) Make new file.
8) Type this text (without minuses):
-------------------------
This is main document.
One
Two
Three
-------------------------

9) Select View-Structure in the main menu
10) Make a new line after 'Three' and press 'Insert subdocument' button on
the 'Structure' toolbar. Select 'SubDocument.doc' and press 'open'.
11) Mark 'One', 'Two' and 'Three' words in main document with style
'MyNumberedList'.
12) Correct missnumbered lists with 'Restart numbering' command and save
document as 'MainDocument.doc'. You will get something like this:
-------------------------
This is main document.
1. One
2. Two
3. Three

This is subdocument.
First list:
1. One
2. Two
3. Three
Second list:
1. One
2. Two
3. Three
-------------------------

13) Close document and then open it.
14) Press 'Expand subdocuments' button on the 'structure' toolbar. You will
get:
-------------------------
This is main document.
1. One
2. Two
3. Three

This is subdocument.
First list:
1. One
2. Two
3. Three
Second list:
4. One
5. Two
6. Three
-------------------------

15) Enjoy. I suggest you try to correct missnumbered list (this will be the
last list) using 'restart numbering' command and see what is happening:
-------------------------
This is main document.
1. One
2. Two
3. Three

This is subdocument.
First list:
4. One
5. Two
6. Three
Second list:
1. One
2. Two
3. Three
-------------------------

Very strange, isn't it?
You can make some direct formatting in 'MainDocument.doc' and
'SubDocument.doc' to see that direct formatting preserved during save
operation but the numbering is not.