I do not think you are being paranoid. Nor do I think his behavior is “natural.” There is nothing natural about talking for hours, almost every day, with another female who is not his significant other. They have apparently developed a close, emotional relationship, one that does not involve you. You would probably feel much better if you were involved in the relationship but you aren’t and that is a problem.
His behavior has actually gotten worse. He used to tell you when she called and when they talked. He no longer tells you. He keeps it a secret and he hides when he is on the phone with her. Now you’re concerned and rightly so. His behavior is deceptive and unacceptable.
Yes, you should talk to him again. He should be willing to convert the relationship he has with her into one that is acceptable to you. If he is not willing to do this then your relationship with him is likely over. Ways he could convert the relationship to be more acceptable to you may include there being no secrecy when she calls, he talks to her on the phone while in the same room with you, or the two of you have her over together, etc. If he can’t abide by the rules that the two of you set, then your relationship with him is already over. If he chooses not to abide by the rules or does not believe that you should be bothered by their relationship, then you may have to face the fact that your relationship is over.
The relationship between you and he should be the most important. If he doesn’t choose your relationship over that of his new friend then you must realize the full impact of his choice. You can’t allow him to demean you by his trying to make you think that you are wrong or jealous. He is being deceitful and secretive. He needs to see the errors of his ways. Perhaps he has found someone that he loves more than you, perhaps he is simply cheating but by any measure–he is wrong to behave as he has been.