Again, in Q & A order:
Q1: Does removing the pre-flight p12 file completely break adobe?
Response: No, it will not completely break Acrobat DC Pro, however removing the P12 certificate will violate the EULA (End User License Agreement).
Q2: I understand the file is necessary for auditing, but will adobe function without the file?
Response: Yes, it will work but the Preflight plug-in may error in some functions.
Q2.a: If not, than why? See response above.