Yes. Your blowout at Agency will immediately register. NAC checks the OPM Security/Suitability Investigations Index (SII), the Defense Clearance and Investigations Index (DCII), the Federal Bureau of Investigation (FBI) Identification Division’s name and fingerprint files, and other files or indices when necessary (noted in your history to check local or state for criminal history). Your previous rejection will register with DCII or SII (depending on who ran it).

Moreover, if you are applying for a SECRET - they will actually do three things...

Run a NAC.
Pull your credit.
Run a NACI (National Agency Check and Inquiry) - in addition to the NAC data, they also pull national criminal history (federal and state level reported crimes) and attempt to send inquiries to at least a few of the people on your SF86 (primary residence reference, the three people you listed as personal references, your employer, etc.)

Again... I strongly advise you not to lie to the new people about your Agency ping... if you're cooked for life - you better find that out now... without ENSURING you're cooked for life by lying to the investigation team.