I Can't see how denial of petition affects the six months period for filing missing parts. If it had been after the six months you would have had to refile the whole thing. If you aren't worried about priority you may do this anyway, but it could confuse foreign filings later. I know this is supposed to be common, but in my 25 years I have never had this problem, even dealing with ex-employees who may have left on unhappy terms.
Speaking of foreign filings, what are your thoughts on provisional applications as priority documents? It appears that most countries accept them and so you might have the filing date of the provisional running against you. I know provisionals were initially set up to get around this, but it seems to put some doubts in some minds. My associate always assumes that he's up against the provisional filing date, and gets his Convention applications on file by that date. I personally don't like provisionals and have only filed a couple. At first the requirements were so much looser, but now you really need a full blown application (less claims) if you plan to rely on it even for US priority, so the applicant is really only saving on the filing fee.