Adding citrus to stew while cooking or after
When citrus juice is added to a soup or sauce, it's usually added at the last minute, after cooking. The reason is that when citrus juice is cooked, it looses some of its flavor.
As Juhasz mentioned, dried beans should not be cooked with acid. Acid will make them take a lot longer to cook. It may also make the skins tough and unpleasant to eat. (Unless you removed the skins, as is sometimes done with fava beans.)
You could possibly use that to your advantage if your fava beans are fully cooked before the rest of the stew is done cooking. Adding an acid might stop the beans from getting too soft while the rest of the stew cooks. (Emphasis on &quot;might;&quot; I'm only guessing about this. All the references I've seen are focused on the goal of getting the beans fully cooked, not on stopping them from cooking too much.)
Summary:
Don't add any citrus or vinegar until the fava beans are fully cooked. If you do add some after that point, expect that the citrus juice will lose some flavor the longer you cook it. Add additional lime juice immediately before serving if you want that bright, fresh taste of lime juice.