First I'm going to link to Jonathan Jarrett's post on the last nuns of Sant Joan de Ripoll, aka Sant Joan de les Abadesses. Go read it; click on the charter and enjoy the lovely script and the impressive collection of signa.
The ousting of the nuns from Sant Joan has always seemed fishy; the counts levelling the accusations against them benefit so clearly that one becomes skeptical. The former abbess Ingilberga, I believe, ended up buried at the altar of St. John in the cathedral of Vic, although I can no longer recall where I read that. It seems a final sign of devotion to her community's saintly patron.
Sant Joan was far from the only nunnery in the Middle Ages to be forcibly closed. Here is one of those cases where I'm sure Jo Ann McNamara's Sisters in Arms describes some other examples, but the lack of a subject index makes it exceedingly difficult to find where. However, my own notes on other houses in Catalonia turns up several others, all from the later Middle Ages.
One house of Hospitaler women, which had only been opened a few years earlier, closed in 1250. Seven women's communities in Catalonia closed between 1307 and 1399; another fourteen closed between 1407 and 1475. There's another group of twelve or so closures in the second half of the sixteenth century.
Why? For many of these I've found very little information so far. Unlike the nuns of Sant Joan, the nuns of these houses were not accused of parricide, and not explicitly called whores either. Where rationales for the houses' closing can be found, the reasons cited are poverty, disrepair, and dwindling numbers that made it difficult or impossible to maintain the monastic rule. Josep Marques discussed seven of them in an article for Estudis del Baix-Emporda 15 (1996). All seven of these houses were small, with relatively few nuns (seven or eight, often becoming fewer over time) and modest endowments. One house was closed when its membership came to consist of the prioress, a single nun, and a servant; another was built in a location prone to flooding. In most cases the remaining nuns joined another community, and the properties and title of prioress would be attached to the other community as well.
Several of the 15th-century closures were Cistercian; these were usually ordered to close by a superior Cistercian abbot, on the grounds that they were too small. In these cases what tended to happen was that the remaining nuns joined a larger Cistercian nunnery, while the property went to Poblet, the large Cistercian men's monastery in Catalonia. That seems a bit hard on the women's communities, who had to take in extra membership without getting extra resources to support them. These closings may be part of a larger pattern of similar phenomena in the 15th century.
In a lot of cases, however, we just don't know what the rationales were. Nor do we know whether there was truth to the reasons claimed, or whether a group of perfectly ordinary nuns fell victim to political and ecclesiastical machinations.