What I’ve managed to discover so far is that Adobe does not offer a Flex/Flash component that is capable of ‘manipulating’ InDesign documents at runtime (but maybe someone can still verify this information). At this moment my conclusion is that in order to achieve this requirement I would have to implement a ‘parser’ that is capable of reading and writing *.idml files (in reality you can consider them as a set of *.xml files contained in a zip package). There is a good place to get started:
IDML File Format Specification
On the other hand there are several companies on the market offering an ‘out-of-the-box’ or a ‘SaaS’ solution. I don’t think I should mention them all here in a public forum - if you’re really interested I can send couple of names through a PM.
Hope this helps!