Do you mean that the formatting goes altogether, or just renumbers and looks a mess?
Word does funny things with automatic bullets - renumbers them at will. Takes some taming - key things are to turn off auto-formatting and customise the bullet so it does (not) follow on from previous bullet numbering.
Could you keep the parts seperate and alter the page numbering starting number? Bit late now, but best to leave the titivation to last - get the words down, proof-read and correct, then make nice.
[edit] Have you maybe defined something that is document specific rather than global - i.e. part of the normal template? Word is terrible for formatting - I have painful memories
