Eventually i think that Flack would always side with the cops as many have pointed out he is a second or third generation cop and so its bred in to him, he does have a good relationship with most of the csi's but i think that when it eventually came down to it, he would side with the cops only if there was a clear reason for exmaple the cop had murdered someone and there is evidence will he reluctinly side with the csis.
I do agree with you La_Guera. I understand his reluctance at first to turn over his notepad. I also thought Mac should have asked the others working the case with him for their notepads. But the second time around when Mac said he needed it, I thought he would have understood where Mac was coming from. I believe how Mac first handled it lead to Flack not wanting to give up the notepad in the first place. And while what the dirty cop did would now be put under scrutiny its better to make sure. But I don't think everything should be over turned as a result either. And I also agree Moran probably didn't get charged.
I agree that Flack is pretty much going to side with cops given the choice--after all, he is one, and he clearly relates more to them than the CSIs. I think he likes the CSIs, but as someone else mentioned, aside from Stella and Danny, he doesn't seem to have personal relationships with any of them. The way he's been at odds with Mac this season is different than how Mac and Danny clashed--Danny clearly craved Mac's approval, but Flack isn't looking for that. He's been trying to do his job and protect his people, and sometimes those desires are at odds with what Mac wants or the evidence shows.
To be honest I think the writers have taken s in a direction that the other CSI's have not. That's prt of why NY has it's appeal. I think Don shows us both sides of the coin, you don't really see Detectives in the other CSI's mixing or having storylines related to their stations. Whatever happens we know that Flack is a stickler for justice so I think he'll side with whatever he believes is right.