Hi Lucas,
Same situation. On April 4th, I was asked to provide RCMP PCC and Hong Kong PCC.
Two weeks later, I uploaded the RCMP one along with an explanation letter that HK PCC will be sent separately. Background check status changed to N/A in a few days.
My Hong Kong PCC is sent from Hong Kong on May 2nd.
Early June I emailed IRCC acquiring the status of my application, to which they applied 'do not need additional information from me'. So I assumed they have received it and are only waiting for an officer to touch my file again.
My background check status remained N/A and changed to IP2 on June 20th.
I had the same concern you do - will my certificate be left forgotten at a dusty corner and officers think I'm missing documents...
But at least you called and tried to find out
I wouldn't be too worried because there had to be previous cases that went through this...email them for peace of mind maybe?
Are you on IP2 now mate?
Regards.