Which one is correct? "He decided that he has had enough and now he regrets it." or "He decided that he had had enough and now he regrets it."
In idea is that a person decided a couple of days ago and today he regrets that decision.
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Note the exact context given by OP's example...
1: He decided that he has had enough and now he regrets it
We can safely assume now there refers to time of utterance. It's irrelevant whether he started being regretful before somebody made the above statement - all that matters is he's currently regretting something.
BUT there's the principle of "backshifting" in English, whereby the following is perfectly natural...
2: Miss Jones said her name was Smith, now she's married to John Smith
(where ...her name is Smith is also perfectly valid, just idiomatically less common)
What this means is that for the specific example, it's entirely a stylistic choice whether to use Present or Past Perfect. But it's worth pointing out that although the word now normally refers "time of utterance", in a Past Tense narrative context it can effectively be used as an alternative to then (the time setting of that past tense narrative).
OP's example muddies the distinction between Past and Present in much the same way as my Miss Jones example (they both report that somebody said/thought something in the past, linked to a statement about the present). If whatever they said in the past is still true, we can optionally choose to report this using Present Tense.
On the other hand, if we change the narrative reference time to the Past, we must use Past Perfect for the initial referent...
3: He decided that he had had enough and now he regretted it
(where Present Perfect he has had enough is invalid in conjunction with Simple Past regretted)
(The decision, the fact of having had enough, and the regret are all in the past.)