Well you do have two accounts there technically, but like you said, one has been closed and the other is in fine standing. It shouldn't affect anything. I can only speak for Paradise 8, Cocoa Casino and This Is Vegas though.
If other Rival casinos are using the mult accounts at Cocoa as a reason for account closing or holding funds then this is completely unjustified and I'll be the first to speak to someone on your behalf about this. If you have multiple accounts at other casinos too though, then it's out of my hands.
As far as being red flagged. It's very possible that the support has made a note on your account after the way you spoke to the CSR you dealt with but it shouldn't affect your account or your ability to deposit/withdraw or claim promos at all.