In the beginning, Angelique's story started simple: she was born in Martinique in the late 1700s, learned voodoo from her mother, and went to Collinsport as a servant with the Dupres family. From there she traveled through time to 1968 (although she may have had a few stops along the way that we didn't see), to 1897, and to 1970.
Then in 1840 we get an Angelique who began life in the late 1600s in the New England town where Judah Zachery did his evil deeds. She went from New England to Martinique. In 1795 she went, as she did originally, from Martinique to Collinsport as a servant with the Dupres family. From 1790s Collinwood, however, she did not proceed to 1968. Instead she plodded through time at the usual rate, apparently, to get to 1840.
What, in the Dark Shadows universe, caused this change? I don't know, but I do know that the last time before 1840 in which we saw Angelique was a very interesting time for her: 1970.
At first in 1970, Angelique was happily married to Sky Rumson, and believed that Diabolos had kept his promise: if she could get a human to fall in love with her, then - oh, I can't remember the details, but she'd live happily ever after, or something. Then she discovered that Sky was a willing part of a scheme of Diabolos (via special agent Nicholas Blair) involving some creatures – the Leviathans – that even Angelique thought were horrific. Suddenly Angelique's on the side of the angels. Very strange. So she splits up with Sky and opposes the Leviathans, which kills the deal she had with Diabolos and also means that she must surely be on Diabolos’s bad side. And yet she is still able to perform witchcraft!
We follow Barnabas from our time band into parallel time, and when we come back to our time band a few months later, Angelique is gone. We get a mention from Quentin of the departure of Chris, Sabrina, and Amy, but he says nothing about Angelique leaving.
And that's as far as I'm going with this. It appears to me there could have been a major upheaval between Diabolos and Angelique in 1970, leading to a change in the fundamental facts of her existence, and possibly a few other fundamental facts as well – but if there was such an upheaval, then we saw nothing of it and know nothing of the details. So it's a big cloud that may not exist anyway, but it's the best that I can come up with.