Acquiring a Z visa in Manila after being rejected in HK

I have been working in China for 10 years (5 in Yantai / 5 in Beijing) and never had any issues with my Z type. Unfortunately during the process of my visa transfer last month, my recent company's HR (Beijing) had neglected filing a document that the new city (Changsha, Hunan) is requiring. Thus, created this suspicion of my legal stay and in short had me travel to Hong Kong to acquire a Z type again and was rejected. I asked HK office why this has happened, all they said was that I should go to my home country (Philippines) and do it from there because being a non-citizen of this country I would be required to produce all of these documents that will just be complicating and a waste of time. He had a point. So when I informed my new employer what had happened, they feared that going to my home country would just complicate things more due to the political situation of our countries and therefore be denied.
I have read in one of your earlier post to a Filipina that you are not aware of any issues that are like that. Understanding that gave me some hope, but I would still like to get your advise or thoughts on my trying in Manila to do this. I am asking because after the rejection in HK I am not feeling confident in trying anymore. Also, what could cause this rejection when you have had no issues for a decade with visas? What reasons could lead to this? Please let me know.