On June 12 you said DHCR gave you specific information on your case. I asked you who said that, but you didn't reply. I'm still interested who at DHCR is giving you this info (I presume over the phone). If you're concerned, please reply using Private Mail.
At this stage, it appears your case is getting complicated. I'd say an active DHCR case should put the court case on hold. I've seen case law on that, but I've also seen cowboy Housing Court judges ignore the law. I'd suggest now to get some legal assistance from a tenant attorney. Holdovers can be tricky - easy to make a mistake.